library(missMethyl)
library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
library(kableExtra)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(dplyr)
ann850k = getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
ann450k = getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
ann450kUnique = ann450k[!(rownames(ann450k) %in% rownames(ann850k)),]
dim(ann450kUnique)
# 33059 33
annAll = rbind(ann850k[,c('Name', 'chr', 'pos', "UCSC_RefGene_Name", "UCSC_RefGene_Group")], ann450kUnique[,c('Name', 'chr', 'pos', "UCSC_RefGene_Name", "UCSC_RefGene_Group")])
annAll = data.frame(annAll)
setwd('/Users/annebozack/Documents/arsenic_meta/generic-metal')
metalProcess = function(table, anno){
colnames(table) = table[1,]
colnames(table)[1] = 'Name'
table = table[-1,]
table = table[,-c(2,3)]
table[,2] = as.numeric(table[,2])
table[,3] = as.numeric(table[,3])
table[,4] = as.numeric(table[,4])
table$P.FDR = p.adjust(table[,4], method='fdr')
table$P.Bonf = p.adjust(table[,4], method='bonferroni')
table = merge(table, annAll, by = 'Name', all.y = F)
table = data.frame(table)
table = table[order(table[,4]),]
return(table)
}
manhattan_meta = function(probe, colors = c("#2D728F", "#2B4162"), FDR = FALSE){
probe$chr = as.numeric(gsub("chr", "", probe$chr))
don = probe %>%
# Compute chromosome size
group_by(chr) %>% summarise(chr_len=as.numeric(max(pos))) %>%
# Calculate cumulative position of each chromosome
mutate(tot=cumsum(chr_len)-chr_len) %>% dplyr::select(-chr_len) %>%
# Add this info to the initial dataset
left_join(probe, ., by=c("chr"="chr")) %>%
# Add a cumulative position of each site
arrange(chr, pos) %>% mutate(poscum=pos+tot) # %>%
# Add highlight and annotation information
# mutate(is_highlight=ifelse(SNP %in% snpsOfInterest, "yes", "no")) %>%
# mutate(is_annotate_fdr=ifelse(adj.P.Val<0.05 & adj.P.Val.bonf>0.05, "yes", "no")) %>%
# mutate(is_annotate_bonf=ifelse(adj.P.Val.bonf <0.05, "yes", "no"))
# don$alpha[don$is_annotate_fdr == 'no'] = 0.6
# don$alpha[don$is_annotate_fdr == 'yes'] = 0
# Prepare X axis
axisdf = don %>% group_by(chr) %>% summarize(center=(max(poscum) + min(poscum))/2)
don = merge(don, probe[,c(1,11)], on='cpg', all.x=T)
if (FDR){
FRDalpha = 0.5
} else {
FRDalpha = 0
}
manhattan = ggplot(don, aes(x=poscum, y=-log10(P.value))) +
geom_point(aes(color=as.factor(chr)), size=0.8, alpha = 0.55) + scale_color_manual(values = rep(colors, dim(table(don$chr)))) +
# p-value cutoffs
geom_hline(yintercept=-log10(0.05/nrow(don)), colour = '#AB3428', size=.3, alpha = 0.5) +
geom_hline(yintercept=-log10(max(don$P.value[don$P.FDR < 0.05])), colour='#AB3428', size=.3, alpha = FRDalpha, linetype = "dashed") +
# custom axes:
scale_x_continuous(expand = c(0.005, 0.005), limits = c(min(don$poscum), max(don$poscum)), label = axisdf$chr, breaks= axisdf$center) +
scale_y_continuous(expand = c(0, 0), limits = c(0, (max(-log10(don$P.value)) + 0.5)), breaks = seq(from = 0, to = (max(-log10(don$P.value)) + 0.5), by = 1)) +
# Custom theme:
theme_minimal() + theme(
legend.position="none", panel.border = element_blank(), panel.grid.minor.y = element_blank(), panel.grid.major.x = element_blank(), panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line(size = 0.2, color = 'gray65')) + theme(text = element_text(size = 7.5)) +
labs(y=expression(-log[10]*"(P-value)"), x='Chromosome')
return(manhattan)
}
lambda <- function(p) median(qchisq(p, df=1, lower.tail=FALSE), na.rm=TRUE) / qchisq(0.5, df=1)
gg_qqplot = function(pvector) {
l = round(lambda(pvector), 3)
o = -log10(sort(pvector, decreasing = FALSE))
e = -log10(ppoints(length(pvector)))
df = data.frame(o = o, e = e)
ggplot(df, aes(e, o)) + geom_point(alpha = 0.5, size = 1) + geom_abline(intercept = 0, slope = 1, color = '#AB3428') + labs(y = expression(Observed ~ ~-log[10](italic(p))), x = expression(Expected ~ ~-log[10](italic(p)))) + theme_classic() + annotate("text", x = 1, y = 5, label = paste0('λ = ', l))
}
volcano_meta = function(probe, FDR = FALSE) {
if (FDR){
FDRalpha = 0.5
} else {
FDRalpha = 0
}
volcano = ggplot(probe, aes(x= Effect, y = -log10(P.value))) +
geom_point(size = 0.8, alpha=0.4) +
geom_hline(aes(yintercept = -log10(0.05/nrow(probe)), color = "#AB3428", alpha = 0.5)) +
geom_hline(aes(yintercept = -log10(max(P.value[P.FDR < 0.05]))), color = "#AB3428", alpha = FDRalpha, linetype = "dashed") + theme_minimal() +
labs(y=expression(-log[10]*"(P-value)"), x='Effect estimate') + theme(panel.grid.minor.y = element_blank()) + theme(text = element_text(size=8)) +
scale_y_continuous(expand = c(0, 0), limits = c(0, (max(-log10(probe$P.value)) + 0.5)), breaks = seq(from = 0, to = (max(-log10(probe$P.value)) + 0.5), by = 1)) +
theme(legend.position="none") + theme(panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line(size = 0.2, color = 'gray65'), panel.grid.major.x = element_line(size = 0.2, color = 'gray65'))
return(volcano)
}
# results adjusted for age, sex, smoking
fact850 = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_850k_092520.txt', sep = "\t", header = T)
fact450 = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_450k_092520.txt', sep = "\t", header = T)
chilePBMC = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_PBMCs_DMPs_updated-results_2020-11-29/age-sex-smoking.txt', sep = "\t", header = T)
chileBuccal = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_buccal_DMPs_updated-results_2020-11-29/age-sex-smoking.txt', sep = "\t", header = T)
allCpg = Reduce(intersect, list(fact850$cpg, fact450$cpg, chilePBMC$cpg, chileBuccal$cpg))
fact850 = fact850[fact850$cpg %in% allCpg,]
fact450 = fact450[fact450$cpg %in% allCpg,]
chilePBMC = chilePBMC[chilePBMC$cpg %in% allCpg,]
chileBuccal = chileBuccal[chileBuccal$cpg %in% allCpg,]
write.table(fact850, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_850k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(fact450, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_450k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chilePBMC, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chileBuccal, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-age-sex-smoking_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
# results adjusted for age, sex, smoking, cells
fact850cell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_850k_092520.txt', sep = "\t", header = T)
fact450cell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_450k_092520.txt', sep = "\t", header = T)
chilePBMCcell = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_PBMCs_DMPs_updated-results_2020-11-29/cell-age-sex-smoking.txt', sep = "\t", header = T)
chileBuccalcell = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_buccal_DMPs_updated-results_2020-11-29/cell-age-sex-smoking.txt', sep = "\t", header = T)
fact850cell = fact850cell[fact850cell$cpg %in% allCpg,]
fact450cell = fact450cell[fact450cell$cpg %in% allCpg,]
chilePBMCcell = chilePBMCcell[chilePBMCcell $cpg %in% allCpg,]
chileBuccalcell = chileBuccalcell[chileBuccalcell$cpg %in% allCpg,]
write.table(fact850cell, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_850k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(fact450cell, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_450k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chilePBMCcell, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chileBuccalcell, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-cell-age-sex-smoking_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
cd /Users/annebozack/Documents/arsenic_meta/generic-metal
MARKER "cpg"
EFFECT "logFC"
PVAL "P.exitValue"
STDERR "std_err"
SCHEME STDERR
# SCHEME STDERR command and weights effect size estimates using the inverse of the corresponding standard errors
# no cell type adjustment, blood only
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/blood_no_cell_common_032921 .tbl
ANALYZE HETEROGENEITY
# no cell type adjustment, all samples
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-age-sex-smoking_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/all_no_cell_common_120420 .tbl
ANALYZE
# cell type adjustment, blood only
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/blood_cell_common_120420 .tbl
ANALYZE
# cell type adjustment, all samples
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-cell-age-sex-smoking_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/all_cell_common_120420 .tbl
ANALYZE
metal_blood_noCell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/blood_no_cell_common_1204201.tbl', sep = "\t")
metal_blood_noCell = metalProcess(metal_blood_noCell)
write.csv(metal_blood_noCell, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DMP_blood_no_cell_common_120420.csv')
# Significant probes
# Nominal P-value
table(metal_blood_noCell$P.value < 0.05)
# FALSE TRUE
# 357719 19632
# FDR
table(metal_blood_noCell$P.FDR < 0.05)
# FALSE
# 377351
table(metal_blood_noCell$P.FDR < 0.1)
# FALSE
# 377351
# Bonferroni
table(metal_blood_noCell$P.Bonf < 0.05)
# FALSE
# 377351
# GO analysis, FDR < 0.1 probes
# NA
# Plotting
gg_qqplot(metal_blood_noCell$P.value)
quartz.save('qq_metal_blood_noCell_120420.png', type = "png", dpi = 300)
manhattan_meta(metal_blood_noCell)
quartz.save('manhattan_metal_blood_noCell_120420.png', type = "png", dpi = 300)
volcano_meta(metal_blood_noCell)
quartz.save('volcano_metal_blood_noCell_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_blood_noCell_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_blood_noCell_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_blood_noCell_120420.png")
| X | Name | Effect | StdErr | P.value | Direction | P.FDR | P.Bonf | chr | pos | UCSC_RefGene_Name | UCSC_RefGene_Group |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 93 | cg00004257 | 0.2473 | 0.0503 | 0.0000009 | +++ | 0.1315697 | 0.3325217 | chr1 | 34629175 | CSMD2 | Body |
| 316516 | cg22938488 | 0.1765 | 0.0365 | 0.0000013 | -++ | 0.1315697 | 0.5045183 | chr5 | 1501670 | LPCAT1 | Body |
| 114376 | cg07490485 | 0.1711 | 0.0356 | 0.0000016 | +++ | 0.1315697 | 0.5924411 | chr14 | 50432614 | ||
| 194923 | cg13490635 | 0.2572 | 0.0537 | 0.0000016 | +++ | 0.1315697 | 0.6207424 | chr8 | 30242021 | RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS | 5’UTR;5’UTR;1stExon;1stExon;1stExon;5’UTR;1stExon;5’UTR |
| 17421 | cg01050273 | -0.2598 | 0.0545 | 0.0000019 | –+ | 0.1315697 | 0.7064011 | chr14 | 101120705 | ||
| 129233 | cg08528486 | 0.1663 | 0.0350 | 0.0000021 | -+- | 0.1315697 | 0.7894183 | chr13 | 113648767 | MCF2L;MCF2L | Body;Body |
| 248565 | cg17342864 | 0.1239 | 0.0268 | 0.0000036 | ++- | 0.1950905 | 1.0000000 | chr2 | 239973967 | HDAC4 | 3’UTR |
| 39707 | cg02483029 | 0.3626 | 0.0795 | 0.0000051 | ++- | 0.2263687 | 1.0000000 | chr8 | 48297271 | KIAA0146 | Body |
| 359036 | cg26299756 | 0.2130 | 0.0468 | 0.0000054 | +++ | 0.2263687 | 1.0000000 | chr6 | 85478807 | ||
| 73319 | cg04685632 | -0.1960 | 0.0437 | 0.0000073 | — | 0.2749002 | 1.0000000 | chr20 | 62082611 | KCNQ2;KCNQ2;KCNQ2;KCNQ2;KCNQ2 | Body;Body;Body;Body;Body |
| 182880 | cg12547807 | -0.2121 | 0.0478 | 0.0000090 | — | 0.2996167 | 1.0000000 | chr1 | 9473751 | ||
| 46132 | cg02892755 | -0.2760 | 0.0627 | 0.0000106 | — | 0.2996167 | 1.0000000 | chr1 | 28103358 | STX12 | Body |
| 233149 | cg16190478 | 0.2482 | 0.0566 | 0.0000118 | +++ | 0.2996167 | 1.0000000 | chr21 | 45789122 | TRPM2 | Body |
| 20130 | cg01218206 | -0.2722 | 0.0621 | 0.0000118 | — | 0.2996167 | 1.0000000 | chr11 | 116933977 | SIK3 | Body |
| 138847 | cg09233730 | 0.1233 | 0.0281 | 0.0000119 | ++- | 0.2996167 | 1.0000000 | chr1 | 1688446 | NADK | Body |
| 290023 | cg20692268 | -0.2330 | 0.0538 | 0.0000146 | — | 0.3155846 | 1.0000000 | chr1 | 25358981 | ||
| 295061 | cg21122375 | -0.2208 | 0.0510 | 0.0000151 | +– | 0.3155846 | 1.0000000 | chr7 | 37956869 | SFRP4 | TSS1500 |
| 3844 | cg00226545 | 0.4875 | 0.1129 | 0.0000158 | +++ | 0.3155846 | 1.0000000 | chr16 | 54320225 | IRX3;IRX3 | 5’UTR;1stExon |
| 297084 | cg21264207 | 0.2006 | 0.0465 | 0.0000159 | +++ | 0.3155846 | 1.0000000 | chr10 | 64576130 | EGR2;EGR2;EGR2;EGR2 | TSS200;5’UTR;TSS200;TSS200 |
| 225228 | cg15572907 | 0.4507 | 0.1050 | 0.0000175 | +++ | 0.3173342 | 1.0000000 | chr19 | 40995921 | SPTBN4 | Body |
| 220977 | cg15206981 | -0.1814 | 0.0423 | 0.0000177 | — | 0.3173342 | 1.0000000 | chr4 | 124323013 | SPRY1;SPRY1 | Body;Body |
| 252559 | cg17679619 | -0.2640 | 0.0617 | 0.0000190 | — | 0.3250364 | 1.0000000 | chr4 | 74542972 | ||
| 110843 | cg07242931 | 0.1968 | 0.0466 | 0.0000242 | ++- | 0.3975311 | 1.0000000 | chr1 | 26034297 | MAN1C1 | Body |
| 316408 | cg22930549 | -0.2602 | 0.0623 | 0.0000297 | — | 0.4198030 | 1.0000000 | chr14 | 68779833 | RAD51L1;RAD51L1;RAD51L1 | Body;Body;Body |
| 330525 | cg24029819 | 0.1850 | 0.0443 | 0.0000299 | +++ | 0.4198030 | 1.0000000 | chr7 | 157550679 | PTPRN2;PTPRN2;PTPRN2 | Body;Body;Body |
| 223120 | cg15396310 | -0.1523 | 0.0366 | 0.0000311 | — | 0.4198030 | 1.0000000 | chr7 | 72971398 | BCL7B | Body |
| 222024 | cg15300814 | 0.1316 | 0.0316 | 0.0000312 | -++ | 0.4198030 | 1.0000000 | chr6 | 111580238 | KIAA1919 | TSS1500 |
| 244019 | cg16994941 | -0.1645 | 0.0395 | 0.0000315 | –+ | 0.4198030 | 1.0000000 | chr5 | 141218887 | ||
| 173665 | cg11832210 | 0.4302 | 0.1036 | 0.0000331 | +++ | 0.4198030 | 1.0000000 | chr10 | 91295346 | SLC16A12 | TSS200 |
| 80050 | cg05137378 | 0.1421 | 0.0343 | 0.0000338 | +++ | 0.4198030 | 1.0000000 | chr1 | 58393137 | DAB1 | 5’UTR |
| 187142 | cg12890388 | 0.1242 | 0.0300 | 0.0000347 | -++ | 0.4198030 | 1.0000000 | chr20 | 10412709 | MKKS;MKKS | 5’UTR;TSS200 |
| 249040 | cg17382048 | -0.2526 | 0.0611 | 0.0000356 | — | 0.4198030 | 1.0000000 | chr11 | 118754386 | CXCR5 | TSS200 |
| 263306 | cg18513383 | 0.1561 | 0.0380 | 0.0000397 | +++ | 0.4277078 | 1.0000000 | chr4 | 57181518 | KIAA1211 | Body |
| 110963 | cg07252171 | 0.1291 | 0.0314 | 0.0000400 | +++ | 0.4277078 | 1.0000000 | chr5 | 573376 | ||
| 182554 | cg12518360 | -0.1890 | 0.0461 | 0.0000408 | — | 0.4277078 | 1.0000000 | chr11 | 92931304 | SLC36A4 | TSS1500 |
| 242633 | cg16876219 | -0.1940 | 0.0475 | 0.0000442 | — | 0.4277078 | 1.0000000 | chr3 | 197222311 | ||
| 139515 | cg09275980 | 0.2946 | 0.0722 | 0.0000446 | +++ | 0.4277078 | 1.0000000 | chr15 | 25350925 | SNORD116-29 | TSS1500 |
| 168526 | cg11434671 | -0.1587 | 0.0389 | 0.0000453 | — | 0.4277078 | 1.0000000 | chr17 | 74524611 | CYGB | 3’UTR |
| 126827 | cg08354093 | 0.2571 | 0.0631 | 0.0000456 | ++- | 0.4277078 | 1.0000000 | chr20 | 23029640 | THBD | 1stExon |
| 70534 | cg04498082 | -0.1478 | 0.0363 | 0.0000474 | — | 0.4277078 | 1.0000000 | chr11 | 356222 | ||
| 74243 | cg04752680 | -0.1173 | 0.0289 | 0.0000482 | — | 0.4277078 | 1.0000000 | chr19 | 14114100 | RFX1 | 5’UTR |
| 69163 | cg04402095 | -0.1163 | 0.0286 | 0.0000484 | — | 0.4277078 | 1.0000000 | chr1 | 156721844 | HDGF;HDGF;HDGF | Body;1stExon;TSS1500 |
| 196521 | cg13586599 | 0.1198 | 0.0295 | 0.0000494 | +++ | 0.4277078 | 1.0000000 | chr6 | 25652383 | SCGN | TSS200 |
| 370510 | cg27144039 | -0.1489 | 0.0369 | 0.0000539 | — | 0.4277078 | 1.0000000 | chr20 | 62605308 | ||
| 304157 | cg21880328 | 0.0981 | 0.0243 | 0.0000546 | +++ | 0.4277078 | 1.0000000 | chr7 | 117514017 | CTTNBP2 | TSS1500 |
| 187085 | cg12884605 | 0.1307 | 0.0324 | 0.0000550 | -++ | 0.4277078 | 1.0000000 | chr12 | 66123314 | ||
| 27848 | cg01729837 | 0.1537 | 0.0381 | 0.0000557 | +++ | 0.4277078 | 1.0000000 | chr19 | 719622 | PALM;PALM | Body;Body |
| 353515 | cg25869889 | 0.1542 | 0.0383 | 0.0000576 | -++ | 0.4277078 | 1.0000000 | chr11 | 6436464 | APBB1;APBB1 | 5’UTR;5’UTR |
| 245138 | cg17083982 | 0.1892 | 0.0472 | 0.0000604 | +++ | 0.4277078 | 1.0000000 | chr12 | 57946083 | KIF5A | Body |
| 372554 | cg27305735 | 0.5261 | 0.1312 | 0.0000609 | -++ | 0.4277078 | 1.0000000 | chr1 | 247537369 | ||
| 351351 | cg25687423 | -0.1458 | 0.0364 | 0.0000618 | — | 0.4277078 | 1.0000000 | chr6 | 43193521 | C6orf108;C6orf108 | Body;3’UTR |
| 308288 | cg22244986 | -0.2426 | 0.0606 | 0.0000620 | — | 0.4277078 | 1.0000000 | chr1 | 201405370 | ||
| 376680 | cg27618777 | -0.2320 | 0.0580 | 0.0000631 | — | 0.4277078 | 1.0000000 | chr6 | 32804628 | TAP2;TAP2 | Body;Body |
| 222274 | cg15323873 | -0.1528 | 0.0382 | 0.0000631 | +– | 0.4277078 | 1.0000000 | chr10 | 79650526 | DLG5 | Body |
| 315429 | cg22853526 | 0.1573 | 0.0393 | 0.0000635 | ++- | 0.4277078 | 1.0000000 | chr1 | 113216965 | MOV10;MOV10 | TSS200;TSS200 |
| 11514 | cg00688297 | -0.3468 | 0.0868 | 0.0000641 | — | 0.4277078 | 1.0000000 | chr8 | 145752292 | LRRC24;MGC70857 | 5’UTR;3’UTR |
| 374551 | cg27455890 | 0.3364 | 0.0843 | 0.0000655 | -+- | 0.4277078 | 1.0000000 | chr10 | 118976677 | ||
| 189609 | cg13100118 | -0.2271 | 0.0569 | 0.0000657 | — | 0.4277078 | 1.0000000 | chr1 | 19795369 | CAPZB | Body |
| 17436 | cg01051581 | -0.1554 | 0.0390 | 0.0000669 | — | 0.4280695 | 1.0000000 | chr5 | 32090639 | PDZD2 | Body |
| 191378 | cg13253153 | 0.1418 | 0.0356 | 0.0000683 | ++- | 0.4293625 | 1.0000000 | chr11 | 2826988 | KCNQ1;KCNQ1 | Body;Body |
| 306721 | cg22111078 | 0.4197 | 0.1058 | 0.0000729 | +++ | 0.4468179 | 1.0000000 | chr5 | 172655925 | ||
| 350973 | cg25652701 | 0.2459 | 0.0621 | 0.0000747 | -++ | 0.4468179 | 1.0000000 | chr7 | 105348517 | ATXN7L1 | Body |
| 278372 | cg19739774 | -0.2022 | 0.0511 | 0.0000766 | — | 0.4468179 | 1.0000000 | chr7 | 7711168 | RPA3 | 5’UTR |
| 270820 | cg19131667 | -0.1760 | 0.0445 | 0.0000779 | — | 0.4468179 | 1.0000000 | chr3 | 17236940 | TBC1D5;TBC1D5;TBC1D5 | Body;Body;Body |
| 140584 | cg09353063 | 0.1687 | 0.0427 | 0.0000779 | +++ | 0.4468179 | 1.0000000 | chr3 | 8811092 | OXTR;OXTR | 1stExon;5’UTR |
| 325184 | cg23618638 | 0.2799 | 0.0709 | 0.0000782 | ++- | 0.4468179 | 1.0000000 | chr7 | 22123315 | ||
| 324549 | cg23558842 | 0.3019 | 0.0766 | 0.0000816 | +++ | 0.4532511 | 1.0000000 | chr11 | 15095178 | CALCB;CALCB | 1stExon;5’UTR |
| 30461 | cg01895740 | 0.1191 | 0.0303 | 0.0000834 | -++ | 0.4532511 | 1.0000000 | chr19 | 7852739 | CLEC4GP1 | Body |
| 115584 | cg07572317 | 0.1241 | 0.0316 | 0.0000842 | -++ | 0.4532511 | 1.0000000 | chr10 | 135029782 | KNDC1 | Body |
| 207752 | cg14276580 | -0.1726 | 0.0439 | 0.0000855 | — | 0.4532511 | 1.0000000 | chr13 | 40527020 | ||
| 28749 | cg01787808 | -0.2151 | 0.0548 | 0.0000871 | — | 0.4532511 | 1.0000000 | chr15 | 34502580 | C15orf29 | TSS1500 |
| 142227 | cg09470219 | 0.1538 | 0.0392 | 0.0000880 | -++ | 0.4532511 | 1.0000000 | chr16 | 22378015 | CDR2 | Body |
| 150380 | cg10079131 | 0.1186 | 0.0303 | 0.0000897 | +++ | 0.4532511 | 1.0000000 | chr11 | 688397 | DEAF1 | Body |
| 96562 | cg06302806 | 0.1502 | 0.0383 | 0.0000898 | -++ | 0.4532511 | 1.0000000 | chr20 | 43939970 | RBPJL | Body |
| 284248 | cg20201957 | 0.1346 | 0.0344 | 0.0000914 | +++ | 0.4532511 | 1.0000000 | chr17 | 2603638 | KIAA0664 | Body |
| 91725 | cg05945266 | 0.1368 | 0.0350 | 0.0000919 | ++- | 0.4532511 | 1.0000000 | chr17 | 80545020 | FOXK2 | Body |
| 65453 | cg04159878 | 0.2325 | 0.0595 | 0.0000933 | -++ | 0.4532511 | 1.0000000 | chr1 | 110179127 | ||
| 4536 | cg00268744 | 0.1620 | 0.0415 | 0.0000944 | ++- | 0.4532511 | 1.0000000 | chr16 | 68281186 | PLA2G15 | Body |
| 228569 | cg15827214 | 0.1445 | 0.0370 | 0.0000949 | -++ | 0.4532511 | 1.0000000 | chr8 | 80522324 | STMN2 | TSS1500 |
| 366745 | cg26870057 | -0.2425 | 0.0622 | 0.0000967 | — | 0.4553062 | 1.0000000 | chr2 | 118947242 | ||
| 301518 | cg21648245 | -0.2749 | 0.0706 | 0.0000988 | –+ | 0.4553062 | 1.0000000 | chr4 | 109541405 | LOC285456;RPL34;RPL34 | Body;TSS1500;TSS1500 |
| 97877 | cg06399735 | 0.1720 | 0.0442 | 0.0000989 | +++ | 0.4553062 | 1.0000000 | chr8 | 18836280 | PSD3 | Body |
| 276528 | cg19599951 | -0.2648 | 0.0682 | 0.0001020 | — | 0.4571093 | 1.0000000 | chr11 | 118754280 | CXCR5 | TSS1500 |
| 250289 | cg17478979 | 0.1844 | 0.0475 | 0.0001022 | -++ | 0.4571093 | 1.0000000 | chr6 | 149772150 | ZC3H12D | Body |
| 186512 | cg12835806 | -0.1459 | 0.0376 | 0.0001045 | — | 0.4571093 | 1.0000000 | chr16 | 2812435 | SRRM2 | Body |
| 261431 | cg18370318 | 0.1477 | 0.0381 | 0.0001063 | +++ | 0.4571093 | 1.0000000 | chr1 | 16258580 | SPEN | Body |
| 17195 | cg01036779 | -0.1355 | 0.0350 | 0.0001064 | — | 0.4571093 | 1.0000000 | chr19 | 6768251 | SH2D3A | TSS1500 |
| 370466 | cg27141509 | -0.2598 | 0.0670 | 0.0001066 | –+ | 0.4571093 | 1.0000000 | chr10 | 5886111 | ||
| 254669 | cg17854066 | 0.1884 | 0.0489 | 0.0001164 | +++ | 0.4806260 | 1.0000000 | chr4 | 55575932 | KIT;KIT | Body;Body |
| 128249 | cg08460812 | -0.2211 | 0.0574 | 0.0001168 | –+ | 0.4806260 | 1.0000000 | chr4 | 109087419 | LOC641518;LEF1;LEF1;LEF1;LEF1 | TSS1500;Body;Body;Body;Body |
| 227288 | cg15720669 | 0.3590 | 0.0933 | 0.0001183 | +++ | 0.4806260 | 1.0000000 | chr3 | 138666040 | FOXL2;C3orf72 | TSS200;TSS200 |
| 108350 | cg07090074 | 0.1832 | 0.0476 | 0.0001185 | +++ | 0.4806260 | 1.0000000 | chr16 | 69457218 | CYB5B | TSS1500 |
| 17258 | cg01041239 | 0.1897 | 0.0493 | 0.0001209 | ++- | 0.4806260 | 1.0000000 | chr18 | 13222581 | C18orf1;C18orf1 | 5’UTR;5’UTR |
| 198286 | cg13692433 | 0.1526 | 0.0397 | 0.0001209 | +++ | 0.4806260 | 1.0000000 | chr11 | 112832159 | NCAM1;NCAM1;NCAM1;NCAM1;NCAM1;NCAM1 | 1stExon;5’UTR;5’UTR;1stExon;5’UTR;1stExon |
| 298451 | cg21405786 | 0.1850 | 0.0481 | 0.0001210 | +++ | 0.4806260 | 1.0000000 | chr7 | 148990485 | ZNF783 | Body |
| 141105 | cg09390241 | -0.1942 | 0.0506 | 0.0001225 | — | 0.4815156 | 1.0000000 | chr4 | 8174148 | ||
| 199983 | cg13802583 | 0.2841 | 0.0741 | 0.0001253 | +++ | 0.4874441 | 1.0000000 | chr12 | 130961453 | RIMBP2 | Body |
| 370211 | cg27123273 | -0.1284 | 0.0335 | 0.0001275 | — | 0.4909414 | 1.0000000 | chr16 | 72405329 | ||
| 76726 | cg04911180 | -0.2970 | 0.0776 | 0.0001295 | –+ | 0.4916344 | 1.0000000 | chr3 | 176775716 | TBL1XR1 | Body |
| 323848 | cg23504707 | 0.1422 | 0.0372 | 0.0001304 | +++ | 0.4916344 | 1.0000000 | chr14 | 60712563 | PPM1A;PPM1A | 5’UTR;1stExon |
metal_all_noCell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/all_no_cell_common_1204201.tbl', sep = "\t")
metal_all_noCell = metalProcess(metal_all_noCell)
write.csv(metal_all_noCell, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DMP_all_no_cell_common_120420.csv')
# Significant probes
# Nominal P-value
table(metal_all_noCell$P.value < 0.05)
# FALSE TRUE
# 356030 21321
# FDR
table(metal_all_noCell$P.FDR < 0.05)
# FALSE
# 377351
table(metal_all_noCell$P.FDR < 0.1)
# FALSE TRUE
# 377348 3
# Bonferroni
table(metal_all_noCell$P.Bonf < 0.05)
# FALSE
# 377351
# GO analysis, FDR < 0.1 probes
annAll2 = rbind(ann850k[,c('Name', 'chr', 'pos', "UCSC_RefGene_Name", "UCSC_RefGene_Group")], ann450kUnique[,c('Name', 'chr', 'pos', "UCSC_RefGene_Name", "UCSC_RefGene_Group")])
go_metal_all_noCell = gometh(sig.cpg = metal_all_noCell$Name[metal_all_noCell$P.FDR < 0.1], all.cpg = metal_all_noCell$Name, array.type = '450K', anno = annAll2)
go_metal_all_noCell = go_metal_all_noCell[order(go_metal_all_noCell$P.DE),]
table(go_metal_all_noCell$P.DE<0.05)
# FALSE TRUE
# 22516 46
table(go_metal_all_noCell$FDR<0.05)
# FALSE
# 22557
write.csv(go_metal_all_noCell[go_metal_all_noCell$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DMP_all_no_cell_common_120420.csv')
# KEGG analysis, FDR < 0.1 probes
kegg_metal_all_noCell = gometh(sig.cpg = metal_all_noCell$Name[metal_all_noCell$P.FDR < 0.1], all.cpg = metal_all_noCell$Name, collection = 'KEGG', array.type = '450K', anno = annAll2)
kegg_metal_all_noCell = kegg_metal_all_noCell[order(kegg_metal_all_noCell$P.DE),]
table(kegg_metal_all_noCell$P.DE<0.05)
# FALSE TRUE
# 338 2
table(kegg_metal_all_noCell$FDR<0.05)
# FALSE
# 340
write.csv(kegg_metal_all_noCell[kegg_metal_all_noCell$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DMP_all_no_cell_common_120420.csv')
# Plotting
gg_qqplot(metal_all_noCell$P.value)
quartz.save('qq_metal_all_noCell_120420.png', type = "png", dpi = 300)
manhattan_meta(metal_all_noCell)
quartz.save('manhattan_metal_all_noCell_120420.png', type = "png", dpi = 300)
volcano_meta(metal_all_noCell)
quartz.save('volcano_metal_all_noCell_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_all_noCell_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_all_noCell_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_all_noCell_120420.png")
| X | Description | N | DE | P.DE | FDR | |
|---|---|---|---|---|---|---|
| 1 | path:hsa00565 | Ether lipid metabolism | 49 | 1 | 0.0039233 | 1 |
| 2 | path:hsa00564 | Glycerophospholipid metabolism | 92 | 1 | 0.0156145 | 1 |
| NA | NA | NA | NA | NA | NA | NA |
| NA.1 | NA | NA | NA | NA | NA | NA |
| NA.2 | NA | NA | NA | NA | NA | NA |
| NA.3 | NA | NA | NA | NA | NA | NA |
| NA.4 | NA | NA | NA | NA | NA | NA |
| NA.5 | NA | NA | NA | NA | NA | NA |
| NA.6 | NA | NA | NA | NA | NA | NA |
| NA.7 | NA | NA | NA | NA | NA | NA |
| NA.8 | NA | NA | NA | NA | NA | NA |
| NA.9 | NA | NA | NA | NA | NA | NA |
| NA.10 | NA | NA | NA | NA | NA | NA |
| NA.11 | NA | NA | NA | NA | NA | NA |
| NA.12 | NA | NA | NA | NA | NA | NA |
| NA.13 | NA | NA | NA | NA | NA | NA |
| NA.14 | NA | NA | NA | NA | NA | NA |
| NA.15 | NA | NA | NA | NA | NA | NA |
| NA.16 | NA | NA | NA | NA | NA | NA |
| NA.17 | NA | NA | NA | NA | NA | NA |
| NA.18 | NA | NA | NA | NA | NA | NA |
| NA.19 | NA | NA | NA | NA | NA | NA |
| NA.20 | NA | NA | NA | NA | NA | NA |
| NA.21 | NA | NA | NA | NA | NA | NA |
| NA.22 | NA | NA | NA | NA | NA | NA |
| NA.23 | NA | NA | NA | NA | NA | NA |
| NA.24 | NA | NA | NA | NA | NA | NA |
| NA.25 | NA | NA | NA | NA | NA | NA |
| NA.26 | NA | NA | NA | NA | NA | NA |
| NA.27 | NA | NA | NA | NA | NA | NA |
| NA.28 | NA | NA | NA | NA | NA | NA |
| NA.29 | NA | NA | NA | NA | NA | NA |
| NA.30 | NA | NA | NA | NA | NA | NA |
| NA.31 | NA | NA | NA | NA | NA | NA |
| NA.32 | NA | NA | NA | NA | NA | NA |
| NA.33 | NA | NA | NA | NA | NA | NA |
| NA.34 | NA | NA | NA | NA | NA | NA |
| NA.35 | NA | NA | NA | NA | NA | NA |
| NA.36 | NA | NA | NA | NA | NA | NA |
| NA.37 | NA | NA | NA | NA | NA | NA |
| NA.38 | NA | NA | NA | NA | NA | NA |
| NA.39 | NA | NA | NA | NA | NA | NA |
| NA.40 | NA | NA | NA | NA | NA | NA |
| NA.41 | NA | NA | NA | NA | NA | NA |
| NA.42 | NA | NA | NA | NA | NA | NA |
| NA.43 | NA | NA | NA | NA | NA | NA |
| NA.44 | NA | NA | NA | NA | NA | NA |
| NA.45 | NA | NA | NA | NA | NA | NA |
| NA.46 | NA | NA | NA | NA | NA | NA |
| NA.47 | NA | NA | NA | NA | NA | NA |
| NA.48 | NA | NA | NA | NA | NA | NA |
| NA.49 | NA | NA | NA | NA | NA | NA |
| NA.50 | NA | NA | NA | NA | NA | NA |
| NA.51 | NA | NA | NA | NA | NA | NA |
| NA.52 | NA | NA | NA | NA | NA | NA |
| NA.53 | NA | NA | NA | NA | NA | NA |
| NA.54 | NA | NA | NA | NA | NA | NA |
| NA.55 | NA | NA | NA | NA | NA | NA |
| NA.56 | NA | NA | NA | NA | NA | NA |
| NA.57 | NA | NA | NA | NA | NA | NA |
| NA.58 | NA | NA | NA | NA | NA | NA |
| NA.59 | NA | NA | NA | NA | NA | NA |
| NA.60 | NA | NA | NA | NA | NA | NA |
| NA.61 | NA | NA | NA | NA | NA | NA |
| NA.62 | NA | NA | NA | NA | NA | NA |
| NA.63 | NA | NA | NA | NA | NA | NA |
| NA.64 | NA | NA | NA | NA | NA | NA |
| NA.65 | NA | NA | NA | NA | NA | NA |
| NA.66 | NA | NA | NA | NA | NA | NA |
| NA.67 | NA | NA | NA | NA | NA | NA |
| NA.68 | NA | NA | NA | NA | NA | NA |
| NA.69 | NA | NA | NA | NA | NA | NA |
| NA.70 | NA | NA | NA | NA | NA | NA |
| NA.71 | NA | NA | NA | NA | NA | NA |
| NA.72 | NA | NA | NA | NA | NA | NA |
| NA.73 | NA | NA | NA | NA | NA | NA |
| NA.74 | NA | NA | NA | NA | NA | NA |
| NA.75 | NA | NA | NA | NA | NA | NA |
| NA.76 | NA | NA | NA | NA | NA | NA |
| NA.77 | NA | NA | NA | NA | NA | NA |
| NA.78 | NA | NA | NA | NA | NA | NA |
| NA.79 | NA | NA | NA | NA | NA | NA |
| NA.80 | NA | NA | NA | NA | NA | NA |
| NA.81 | NA | NA | NA | NA | NA | NA |
| NA.82 | NA | NA | NA | NA | NA | NA |
| NA.83 | NA | NA | NA | NA | NA | NA |
| NA.84 | NA | NA | NA | NA | NA | NA |
| NA.85 | NA | NA | NA | NA | NA | NA |
| NA.86 | NA | NA | NA | NA | NA | NA |
| NA.87 | NA | NA | NA | NA | NA | NA |
| NA.88 | NA | NA | NA | NA | NA | NA |
| NA.89 | NA | NA | NA | NA | NA | NA |
| NA.90 | NA | NA | NA | NA | NA | NA |
| NA.91 | NA | NA | NA | NA | NA | NA |
| NA.92 | NA | NA | NA | NA | NA | NA |
| NA.93 | NA | NA | NA | NA | NA | NA |
| NA.94 | NA | NA | NA | NA | NA | NA |
| NA.95 | NA | NA | NA | NA | NA | NA |
| NA.96 | NA | NA | NA | NA | NA | NA |
| NA.97 | NA | NA | NA | NA | NA | NA |
| X | ONTOLOGY | TERM | N | DE | P.DE | FDR | |
|---|---|---|---|---|---|---|---|
| 1 | GO:0047191 | MF | 1-alkylglycerophosphocholine O-acyltransferase activity | 1 | 1 | 0.0009633 | 1 |
| 2 | GO:2001246 | BP | negative regulation of phosphatidylcholine biosynthetic process | 1 | 1 | 0.0009633 | 1 |
| 3 | GO:0047159 | MF | 1-alkenylglycerophosphocholine O-acyltransferase activity | 2 | 1 | 0.0009633 | 1 |
| 4 | GO:0050200 | MF | plasmalogen synthase activity | 2 | 1 | 0.0009633 | 1 |
| 5 | GO:0047192 | MF | 1-alkylglycerophosphocholine O-acetyltransferase activity | 3 | 1 | 0.0010256 | 1 |
| 6 | GO:0047184 | MF | 1-acylglycerophosphocholine O-acyltransferase activity | 4 | 1 | 0.0010256 | 1 |
| 7 | GO:0016413 | MF | O-acetyltransferase activity | 7 | 1 | 0.0014116 | 1 |
| 8 | GO:2001245 | BP | regulation of phosphatidylcholine biosynthetic process | 5 | 1 | 0.0016745 | 1 |
| 9 | GO:0036148 | BP | phosphatidylglycerol acyl-chain remodeling | 18 | 1 | 0.0018954 | 1 |
| 10 | GO:0043129 | BP | surfactant homeostasis | 9 | 1 | 0.0020195 | 1 |
| 11 | GO:0048875 | BP | chemical homeostasis within a tissue | 11 | 1 | 0.0020229 | 1 |
| 12 | GO:0036151 | BP | phosphatidylcholine acyl-chain remodeling | 29 | 1 | 0.0027444 | 1 |
| 13 | GO:0150172 | BP | regulation of phosphatidylcholine metabolic process | 8 | 1 | 0.0029006 | 1 |
| 14 | GO:0003841 | MF | 1-acylglycerol-3-phosphate O-acyltransferase activity | 13 | 1 | 0.0038687 | 1 |
| 15 | GO:0016411 | MF | acylglycerol O-acyltransferase activity | 19 | 1 | 0.0038688 | 1 |
| 16 | GO:0046471 | BP | phosphatidylglycerol metabolic process | 33 | 1 | 0.0040670 | 1 |
| 17 | GO:0071072 | BP | negative regulation of phospholipid biosynthetic process | 7 | 1 | 0.0042526 | 1 |
| 18 | GO:0042171 | MF | lysophosphatidic acid acyltransferase activity | 15 | 1 | 0.0043004 | 1 |
| 19 | GO:0071617 | MF | lysophospholipid acyltransferase activity | 17 | 1 | 0.0043626 | 1 |
| 20 | GO:0035577 | CC | azurophil granule membrane | 54 | 1 | 0.0048208 | 1 |
| 21 | GO:0008374 | MF | O-acyltransferase activity | 42 | 1 | 0.0058474 | 1 |
| 22 | GO:0071071 | BP | regulation of phospholipid biosynthetic process | 19 | 1 | 0.0063761 | 1 |
| 23 | GO:1903726 | BP | negative regulation of phospholipid metabolic process | 13 | 1 | 0.0063958 | 1 |
| 24 | GO:0006656 | BP | phosphatidylcholine biosynthetic process | 38 | 1 | 0.0076155 | 1 |
| 25 | GO:0016407 | MF | acetyltransferase activity | 92 | 1 | 0.0080324 | 1 |
| 26 | GO:0006654 | BP | phosphatidic acid biosynthetic process | 47 | 1 | 0.0099298 | 1 |
| 27 | GO:0051055 | BP | negative regulation of lipid biosynthetic process | 54 | 1 | 0.0099924 | 1 |
| 28 | GO:0046473 | BP | phosphatidic acid metabolic process | 49 | 1 | 0.0104286 | 1 |
| 29 | GO:0005811 | CC | lipid droplet | 85 | 1 | 0.0106104 | 1 |
| 30 | GO:0046470 | BP | phosphatidylcholine metabolic process | 86 | 1 | 0.0123996 | 1 |
| 31 | GO:0005766 | CC | primary lysosome | 142 | 1 | 0.0138020 | 1 |
| 32 | GO:0042582 | CC | azurophil granule | 142 | 1 | 0.0138020 | 1 |
| 33 | GO:0045833 | BP | negative regulation of lipid metabolic process | 93 | 1 | 0.0165409 | 1 |
| 34 | GO:0016747 | MF | transferase activity, transferring acyl groups other than amino-acyl groups | 200 | 1 | 0.0197092 | 1 |
| 35 | GO:0016746 | MF | transferase activity, transferring acyl groups | 228 | 1 | 0.0214958 | 1 |
| 36 | GO:1903725 | BP | regulation of phospholipid metabolic process | 90 | 1 | 0.0237582 | 1 |
| 37 | GO:0046890 | BP | regulation of lipid biosynthetic process | 197 | 1 | 0.0338788 | 1 |
| 38 | GO:0060041 | BP | retina development in camera-type eye | 147 | 1 | 0.0369490 | 1 |
| 39 | GO:0046474 | BP | glycerophospholipid biosynthetic process | 218 | 1 | 0.0376870 | 1 |
| 40 | GO:0045732 | BP | positive regulation of protein catabolic process | 209 | 1 | 0.0380340 | 1 |
| 41 | GO:0008654 | BP | phospholipid biosynthetic process | 259 | 1 | 0.0413918 | 1 |
| 42 | GO:0045017 | BP | glycerolipid biosynthetic process | 251 | 1 | 0.0431814 | 1 |
| 43 | GO:0030667 | CC | secretory granule membrane | 292 | 1 | 0.0436461 | 1 |
| 44 | GO:0001894 | BP | tissue homeostasis | 246 | 1 | 0.0447369 | 1 |
| 45 | GO:0005765 | CC | lysosomal membrane | 353 | 1 | 0.0484312 | 1 |
| 46 | GO:0098852 | CC | lytic vacuole membrane | 353 | 1 | 0.0484312 | 1 |
| NA | NA | NA | NA | NA | NA | NA | NA |
| NA.1 | NA | NA | NA | NA | NA | NA | NA |
| NA.2 | NA | NA | NA | NA | NA | NA | NA |
| NA.3 | NA | NA | NA | NA | NA | NA | NA |
| NA.4 | NA | NA | NA | NA | NA | NA | NA |
| NA.5 | NA | NA | NA | NA | NA | NA | NA |
| NA.6 | NA | NA | NA | NA | NA | NA | NA |
| NA.7 | NA | NA | NA | NA | NA | NA | NA |
| NA.8 | NA | NA | NA | NA | NA | NA | NA |
| NA.9 | NA | NA | NA | NA | NA | NA | NA |
| NA.10 | NA | NA | NA | NA | NA | NA | NA |
| NA.11 | NA | NA | NA | NA | NA | NA | NA |
| NA.12 | NA | NA | NA | NA | NA | NA | NA |
| NA.13 | NA | NA | NA | NA | NA | NA | NA |
| NA.14 | NA | NA | NA | NA | NA | NA | NA |
| NA.15 | NA | NA | NA | NA | NA | NA | NA |
| NA.16 | NA | NA | NA | NA | NA | NA | NA |
| NA.17 | NA | NA | NA | NA | NA | NA | NA |
| NA.18 | NA | NA | NA | NA | NA | NA | NA |
| NA.19 | NA | NA | NA | NA | NA | NA | NA |
| NA.20 | NA | NA | NA | NA | NA | NA | NA |
| NA.21 | NA | NA | NA | NA | NA | NA | NA |
| NA.22 | NA | NA | NA | NA | NA | NA | NA |
| NA.23 | NA | NA | NA | NA | NA | NA | NA |
| NA.24 | NA | NA | NA | NA | NA | NA | NA |
| NA.25 | NA | NA | NA | NA | NA | NA | NA |
| NA.26 | NA | NA | NA | NA | NA | NA | NA |
| NA.27 | NA | NA | NA | NA | NA | NA | NA |
| NA.28 | NA | NA | NA | NA | NA | NA | NA |
| NA.29 | NA | NA | NA | NA | NA | NA | NA |
| NA.30 | NA | NA | NA | NA | NA | NA | NA |
| NA.31 | NA | NA | NA | NA | NA | NA | NA |
| NA.32 | NA | NA | NA | NA | NA | NA | NA |
| NA.33 | NA | NA | NA | NA | NA | NA | NA |
| NA.34 | NA | NA | NA | NA | NA | NA | NA |
| NA.35 | NA | NA | NA | NA | NA | NA | NA |
| NA.36 | NA | NA | NA | NA | NA | NA | NA |
| NA.37 | NA | NA | NA | NA | NA | NA | NA |
| NA.38 | NA | NA | NA | NA | NA | NA | NA |
| NA.39 | NA | NA | NA | NA | NA | NA | NA |
| NA.40 | NA | NA | NA | NA | NA | NA | NA |
| NA.41 | NA | NA | NA | NA | NA | NA | NA |
| NA.42 | NA | NA | NA | NA | NA | NA | NA |
| NA.43 | NA | NA | NA | NA | NA | NA | NA |
| NA.44 | NA | NA | NA | NA | NA | NA | NA |
| NA.45 | NA | NA | NA | NA | NA | NA | NA |
| NA.46 | NA | NA | NA | NA | NA | NA | NA |
| NA.47 | NA | NA | NA | NA | NA | NA | NA |
| NA.48 | NA | NA | NA | NA | NA | NA | NA |
| NA.49 | NA | NA | NA | NA | NA | NA | NA |
| NA.50 | NA | NA | NA | NA | NA | NA | NA |
| NA.51 | NA | NA | NA | NA | NA | NA | NA |
| NA.52 | NA | NA | NA | NA | NA | NA | NA |
| NA.53 | NA | NA | NA | NA | NA | NA | NA |
metal_blood_cell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/blood_cell_common_1204201.tbl', sep = "\t")
metal_blood_cell = metalProcess(metal_blood_cell)
write.csv(metal_blood_cell, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DMP_blood_cell_common_120420.csv')
# Significant probes
# Nominal P-value
table(metal_blood_cell$P.value < 0.05)
# FALSE TRUE
# 353990 23361
# FDR
table(metal_blood_cell$P.FDR < 0.05)
# FALSE TRUE
# 377350 1
table(metal_blood_cell$P.FDR < 0.1)
# FALSE TRUE
# 377343 8
# Bonferroni
table(metal_blood_cell$P.Bonf < 0.05)
# FALSE TRUE
# 377350 1
# GO analysis, nominally-significant probes
go_metal_blood_cell = gometh(sig.cpg = metal_blood_cell$Name[metal_blood_cell$P.FDR < 0.1], all.cpg = metal_blood_cell$Name, array.type = '450K', sig.genes = T, anno = annAll2)
go_metal_blood_cell = go_metal_blood_cell[order(go_metal_blood_cell$P.DE),]
table(go_metal_blood_cell$P.DE<0.05)
# FALSE TRUE
# 22131 452
table(go_metal_blood_cell$FDR<0.05)
# FALSE
# 22583
write.csv(go_metal_blood_cell[go_metal_blood_cell$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DMP_blood_cell_common_120420.csv')
# KEGG analysis, nominally-significant probes
kegg_metal_blood_cell = gometh(sig.cpg = metal_blood_cell$Name[metal_blood_cell$P.FDR < 0.1], all.cpg = metal_blood_cell$Name, array.type = '450K', collection = 'KEGG', sig.genes = T, anno = annAll2)
kegg_metal_blood_cell = kegg_metal_blood_cell[order(kegg_metal_blood_cell$P.DE),]
table(kegg_metal_blood_cell$P.DE<0.05)
# FALSE TRUE
# 337 3
table(kegg_metal_blood_cell$FDR<0.05)
# FALSE
# 340
write.csv(kegg_metal_blood_cell[c(1:20),], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DMP_blood_cell_common_120420.csv')
# Plotting
gg_qqplot(metal_blood_cell$P.value)
quartz.save('qq_metal_blood_cell_120420.png', type = "png", dpi = 300)
manhattan_meta(metal_blood_cell)
quartz.save('manhattan_metal_blood_cell_120420.png', type = "png", dpi = 300)
volcano_meta(metal_blood_cell)
quartz.save('volcano_metal_blood_cell_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_blood_cell_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_blood_cell_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_blood_cell_120420.png")
| X | Name | Effect | StdErr | P.value | Direction | P.FDR | P.Bonf | chr | pos | UCSC_RefGene_Name | UCSC_RefGene_Group |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 194923 | cg13490635 | 0.3069 | 0.0567 | 1.00e-07 | +++ | 0.0237656 | 0.0237656 | chr8 | 30242021 | RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS | 5’UTR;5’UTR;1stExon;1stExon;1stExon;5’UTR;1stExon;5’UTR |
| 186512 | cg12835806 | -0.2055 | 0.0408 | 5.00e-07 | — | 0.0861304 | 0.1819964 | chr16 | 2812435 | SRRM2 | Body |
| 143925 | cg09595163 | 0.5056 | 0.1019 | 7.00e-07 | +++ | 0.0861304 | 0.2655796 | chr3 | 55515541 | WNT5A | Body |
| 360597 | cg26412543 | -0.2648 | 0.0540 | 1.00e-06 | — | 0.0861304 | 0.3598419 | chr6 | 32128829 | PPT2;PPT2 | Body;Body |
| 44706 | cg02799448 | 0.1687 | 0.0351 | 1.50e-06 | -++ | 0.0861304 | 0.5607436 | chr6 | 137817008 | OLIG3 | TSS1500 |
| 95521 | cg06218338 | 0.3073 | 0.0641 | 1.60e-06 | -++ | 0.0861304 | 0.6181009 | chr7 | 27231894 | ||
| 353232 | cg25840057 | -0.1794 | 0.0375 | 1.70e-06 | +– | 0.0861304 | 0.6456476 | chr13 | 113730354 | MCF2L;MCF2L | Body;Body |
| 220977 | cg15206981 | -0.2178 | 0.0456 | 1.80e-06 | — | 0.0861304 | 0.6890429 | chr4 | 124323013 | SPRY1;SPRY1 | Body;Body |
| 30961 | cg01927825 | -0.3417 | 0.0725 | 2.50e-06 | — | 0.1032265 | 0.9290382 | chr1 | 2121724 | C1orf86;LOC100128003;C1orf86 | Body;Body;Body |
| 222521 | cg15345437 | -0.1694 | 0.0362 | 2.90e-06 | — | 0.1046133 | 1.0000000 | chr11 | 62620843 | SNORD22;SNORD31;SNHG1 | TSS1500;Body;Body |
| 201470 | cg13900348 | 0.3509 | 0.0755 | 3.40e-06 | +++ | 0.1046133 | 1.0000000 | chr5 | 76114646 | F2RL1 | TSS200 |
| 20130 | cg01218206 | -0.2163 | 0.0467 | 3.60e-06 | — | 0.1046133 | 1.0000000 | chr11 | 116933977 | SIK3 | Body |
| 286295 | cg20380069 | 0.1757 | 0.0379 | 3.60e-06 | +++ | 0.1046133 | 1.0000000 | chr12 | 120806617 | MSI1 | Body |
| 2859 | cg00160440 | -0.1362 | 0.0297 | 4.50e-06 | — | 0.1202402 | 1.0000000 | chr4 | 134077575 | PCDH10 | Body |
| 64145 | cg04080022 | -0.1951 | 0.0430 | 5.80e-06 | — | 0.1363416 | 1.0000000 | chr16 | 89648534 | CPNE7;CPNE7 | Body;Body |
| 96670 | cg06313349 | -0.2251 | 0.0496 | 5.80e-06 | — | 0.1363416 | 1.0000000 | chr7 | 157494424 | PTPRN2;PTPRN2;PTPRN2 | Body;Body;Body |
| 173665 | cg11832210 | 0.4809 | 0.1069 | 6.80e-06 | +++ | 0.1513178 | 1.0000000 | chr10 | 91295346 | SLC16A12 | TSS200 |
| 48278 | cg03025061 | -0.1950 | 0.0437 | 8.00e-06 | — | 0.1566950 | 1.0000000 | chr8 | 109261275 | EIF3E | TSS1500 |
| 184123 | cg12637057 | 0.2537 | 0.0569 | 8.10e-06 | +++ | 0.1566950 | 1.0000000 | chr20 | 59967284 | CDH4 | Body |
| 145527 | cg09714379 | 0.2894 | 0.0649 | 8.30e-06 | +++ | 0.1566950 | 1.0000000 | chr10 | 135044040 | UTF1 | 1stExon |
| 35348 | cg02206980 | -0.5285 | 0.1199 | 1.04e-05 | — | 0.1855881 | 1.0000000 | chr6 | 13574034 | SIRT5;SIRT5 | TSS1500;TSS1500 |
| 176796 | cg12065616 | -0.1729 | 0.0393 | 1.08e-05 | — | 0.1855881 | 1.0000000 | chr12 | 94954828 | ||
| 61580 | cg03906434 | 0.3445 | 0.0794 | 1.45e-05 | -++ | 0.2168360 | 1.0000000 | chr7 | 27231819 | ||
| 114412 | cg07492924 | -0.3742 | 0.0863 | 1.47e-05 | — | 0.2168360 | 1.0000000 | chr16 | 433825 | LOC100134368 | Body |
| 291217 | cg20784693 | -0.5836 | 0.1347 | 1.47e-05 | — | 0.2168360 | 1.0000000 | chr2 | 239984030 | HDAC4 | Body |
| 85525 | cg05507514 | -0.1798 | 0.0416 | 1.55e-05 | — | 0.2168360 | 1.0000000 | chr3 | 153842846 | SGEF | Body |
| 50150 | cg03149958 | -0.1844 | 0.0427 | 1.58e-05 | — | 0.2168360 | 1.0000000 | chr6 | 36326677 | ||
| 279928 | cg19851029 | 0.1962 | 0.0456 | 1.68e-05 | +++ | 0.2168360 | 1.0000000 | chr3 | 138669137 | C3orf72 | Body |
| 178323 | cg12174276 | 0.1279 | 0.0297 | 1.69e-05 | +++ | 0.2168360 | 1.0000000 | chr6 | 166401921 | LOC441177;C6orf176;C6orf176 | Body;TSS1500;TSS1500 |
| 200512 | cg13837335 | -0.1365 | 0.0319 | 1.81e-05 | — | 0.2168360 | 1.0000000 | chr9 | 2191798 | SMARCA2;SMARCA2 | Body;Body |
| 133800 | cg08856347 | 0.2545 | 0.0596 | 1.94e-05 | +++ | 0.2168360 | 1.0000000 | chr2 | 289390 | FAM150B | TSS1500 |
| 187357 | cg12908187 | 0.1873 | 0.0439 | 1.94e-05 | -++ | 0.2168360 | 1.0000000 | chr16 | 88450261 | ||
| 373928 | cg27406919 | -0.1801 | 0.0422 | 1.95e-05 | — | 0.2168360 | 1.0000000 | chr16 | 87212733 | ||
| 201996 | cg13928490 | -0.2502 | 0.0586 | 1.95e-05 | — | 0.2168360 | 1.0000000 | chr13 | 51640442 | GUCY1B2 | TSS200 |
| 46686 | cg02925222 | 0.1116 | 0.0264 | 2.29e-05 | +++ | 0.2168360 | 1.0000000 | chr11 | 280445 | NLRP6 | Body |
| 92037 | cg05965902 | 0.1887 | 0.0446 | 2.31e-05 | +++ | 0.2168360 | 1.0000000 | chr13 | 21635727 | LATS2 | TSS200 |
| 23933 | cg01464730 | -0.7699 | 0.1821 | 2.35e-05 | — | 0.2168360 | 1.0000000 | chr17 | 78809873 | RPTOR;RPTOR | Body;Body |
| 168281 | cg11414610 | -0.1493 | 0.0353 | 2.38e-05 | — | 0.2168360 | 1.0000000 | chr19 | 16528319 | EPS15L1 | Body |
| 254158 | cg17819053 | 0.1555 | 0.0368 | 2.38e-05 | +++ | 0.2168360 | 1.0000000 | chr1 | 119549626 | ||
| 347007 | cg25330878 | -0.1506 | 0.0357 | 2.48e-05 | — | 0.2168360 | 1.0000000 | chr17 | 17379109 | MED9 | TSS1500 |
| 131753 | cg08706492 | 0.2375 | 0.0564 | 2.57e-05 | +++ | 0.2168360 | 1.0000000 | chr1 | 247374357 | ||
| 4731 | cg00284153 | -0.1746 | 0.0415 | 2.57e-05 | — | 0.2168360 | 1.0000000 | chr10 | 135171713 | C10orf125;C10orf125 | TSS200;TSS200 |
| 306721 | cg22111078 | 0.4708 | 0.1119 | 2.60e-05 | +++ | 0.2168360 | 1.0000000 | chr5 | 172655925 | ||
| 198286 | cg13692433 | 0.1821 | 0.0433 | 2.65e-05 | +++ | 0.2168360 | 1.0000000 | chr11 | 112832159 | NCAM1;NCAM1;NCAM1;NCAM1;NCAM1;NCAM1 | 1stExon;5’UTR;5’UTR;1stExon;5’UTR;1stExon |
| 282053 | cg20011402 | 0.3952 | 0.0941 | 2.66e-05 | +++ | 0.2168360 | 1.0000000 | chr10 | 17496239 | ST8SIA6 | 1stExon |
| 236494 | cg16427033 | -0.1492 | 0.0355 | 2.70e-05 | +– | 0.2168360 | 1.0000000 | chr10 | 109023583 | ||
| 363371 | cg26623444 | 0.1747 | 0.0416 | 2.73e-05 | +++ | 0.2168360 | 1.0000000 | chr7 | 31376092 | ||
| 228619 | cg15830431 | 0.1666 | 0.0398 | 2.78e-05 | ++- | 0.2168360 | 1.0000000 | chr8 | 99952591 | ||
| 166619 | cg11289100 | 0.2363 | 0.0565 | 2.86e-05 | +++ | 0.2168360 | 1.0000000 | chr17 | 19313024 | RNF112 | TSS1500 |
| 199780 | cg13791254 | 0.5591 | 0.1338 | 2.93e-05 | -++ | 0.2168360 | 1.0000000 | chr9 | 100616607 | FOXE1 | 1stExon |
| 321357 | cg23300529 | -0.1586 | 0.0380 | 3.01e-05 | — | 0.2168360 | 1.0000000 | chr8 | 21989012 | HR;HR | TSS1500;TSS1500 |
| 353248 | cg25840780 | -0.3055 | 0.0733 | 3.12e-05 | — | 0.2168360 | 1.0000000 | chr20 | 50156843 | NFATC2;NFATC2;NFATC2 | Body;Body;Body |
| 193620 | cg13415566 | -0.3939 | 0.0947 | 3.18e-05 | — | 0.2168360 | 1.0000000 | chr10 | 125423240 | ||
| 295061 | cg21122375 | -0.2285 | 0.0550 | 3.22e-05 | — | 0.2168360 | 1.0000000 | chr7 | 37956869 | SFRP4 | TSS1500 |
| 312496 | cg22621867 | 0.3367 | 0.0811 | 3.27e-05 | +++ | 0.2168360 | 1.0000000 | chr3 | 51990301 | GPR62 | 1stExon |
| 291688 | cg20824761 | 0.5956 | 0.1434 | 3.28e-05 | +++ | 0.2168360 | 1.0000000 | chr15 | 69591567 | PAQR5 | 5’UTR |
| 250912 | cg17523124 | 0.1690 | 0.0408 | 3.40e-05 | +++ | 0.2168360 | 1.0000000 | chr20 | 24451769 | TMEM90B | 5’UTR |
| 304218 | cg21885638 | -0.1303 | 0.0315 | 3.45e-05 | — | 0.2168360 | 1.0000000 | chr3 | 129306552 | PLXND1 | Body |
| 72911 | cg04658543 | 0.2106 | 0.0509 | 3.51e-05 | +++ | 0.2168360 | 1.0000000 | chr12 | 113904848 | LHX5 | Body |
| 118338 | cg07766612 | 0.4675 | 0.1131 | 3.57e-05 | +++ | 0.2168360 | 1.0000000 | chr1 | 26372887 | SLC30A2;SLC30A2 | TSS1500;TSS1500 |
| 265230 | cg18672986 | 0.3001 | 0.0727 | 3.66e-05 | +++ | 0.2168360 | 1.0000000 | chr19 | 35521772 | SCN1B;SCN1B | Body;Body |
| 110684 | cg07232688 | -0.1766 | 0.0428 | 3.66e-05 | — | 0.2168360 | 1.0000000 | chr1 | 100644688 | LRRC39 | TSS1500 |
| 316250 | cg22915154 | -0.2157 | 0.0523 | 3.69e-05 | — | 0.2168360 | 1.0000000 | chr11 | 68816030 | TPCN2 | TSS1500 |
| 292390 | cg20899625 | -0.1458 | 0.0354 | 3.78e-05 | — | 0.2168360 | 1.0000000 | chr3 | 126721131 | PLXNA1 | Body |
| 180848 | cg12392225 | -0.1565 | 0.0380 | 3.79e-05 | — | 0.2168360 | 1.0000000 | chr2 | 3464066 | TTC15 | Body |
| 86791 | cg05600350 | 0.4214 | 0.1023 | 3.82e-05 | +++ | 0.2168360 | 1.0000000 | chr4 | 4858598 | ||
| 295936 | cg21185289 | 0.4583 | 0.1113 | 3.85e-05 | +++ | 0.2168360 | 1.0000000 | chr2 | 74743437 | TLX2 | 3’UTR |
| 225228 | cg15572907 | 0.4958 | 0.1206 | 3.97e-05 | +++ | 0.2171135 | 1.0000000 | chr19 | 40995921 | SPTBN4 | Body |
| 354980 | cg25996001 | -0.1629 | 0.0396 | 3.97e-05 | — | 0.2171135 | 1.0000000 | chr15 | 23003087 | CYFIP1;CYFIP1 | 3’UTR;3’UTR |
| 73319 | cg04685632 | -0.1611 | 0.0393 | 4.15e-05 | — | 0.2178127 | 1.0000000 | chr20 | 62082611 | KCNQ2;KCNQ2;KCNQ2;KCNQ2;KCNQ2 | Body;Body;Body;Body;Body |
| 343981 | cg25076597 | -0.3534 | 0.0862 | 4.15e-05 | — | 0.2178127 | 1.0000000 | chr10 | 134150581 | LRRC27;LRRC27;LRRC27;LRRC27;LRRC27 | Body;TSS200;Body;Body;Body |
| 90057 | cg05837401 | 0.2287 | 0.0558 | 4.17e-05 | +++ | 0.2178127 | 1.0000000 | chr3 | 125899086 | ALDH1L1 | 5’UTR |
| 5363 | cg00321074 | -0.1290 | 0.0316 | 4.41e-05 | — | 0.2178127 | 1.0000000 | chr3 | 19990693 | RAB5A | 5’UTR |
| 136595 | cg09064848 | 0.2053 | 0.0503 | 4.41e-05 | +++ | 0.2178127 | 1.0000000 | chr17 | 3627007 | ITGAE;GSG2 | Body;TSS200 |
| 219413 | cg15083775 | 0.1410 | 0.0345 | 4.42e-05 | –+ | 0.2178127 | 1.0000000 | chr17 | 48054048 | ||
| 297867 | cg21344215 | 0.1552 | 0.0380 | 4.47e-05 | +++ | 0.2178127 | 1.0000000 | chr2 | 27851972 | GPN1;CCDC121;CCDC121;GPN1;CCDC121;GPN1;GPN1;GPN1 | 5’UTR;TSS1500;TSS200;Body;TSS1500;5’UTR;Body;1stExon |
| 5575 | cg00333154 | 0.3250 | 0.0797 | 4.53e-05 | +++ | 0.2178127 | 1.0000000 | chr6 | 106808703 | ||
| 2422 | cg00133970 | -0.2104 | 0.0516 | 4.56e-05 | — | 0.2178127 | 1.0000000 | chr7 | 44123200 | POLM | TSS1500 |
| 214534 | cg14709833 | 0.3309 | 0.0812 | 4.56e-05 | +++ | 0.2178127 | 1.0000000 | chr13 | 112157732 | ||
| 34800 | cg02166532 | 0.1862 | 0.0457 | 4.68e-05 | +++ | 0.2207503 | 1.0000000 | chr11 | 2159853 | INS-IGF2;IGF2;IGF2;IGF2;IGF2 | Body;Body;5’UTR;5’UTR;1stExon |
| 260043 | cg18259339 | -0.2166 | 0.0534 | 4.96e-05 | — | 0.2260924 | 1.0000000 | chr17 | 76441793 | DNAH17 | Body |
| 168429 | cg11425470 | -0.1835 | 0.0452 | 4.97e-05 | — | 0.2260924 | 1.0000000 | chr1 | 109271795 | FNDC7 | Body |
| 324549 | cg23558842 | 0.3088 | 0.0761 | 4.97e-05 | +++ | 0.2260924 | 1.0000000 | chr11 | 15095178 | CALCB;CALCB | 1stExon;5’UTR |
| 331371 | cg24090911 | -0.2089 | 0.0516 | 5.13e-05 | — | 0.2273111 | 1.0000000 | chr5 | 400732 | AHRR | Body |
| 180577 | cg12368188 | 0.3807 | 0.0941 | 5.17e-05 | +++ | 0.2273111 | 1.0000000 | chr15 | 67326082 | ||
| 93 | cg00004257 | 0.2348 | 0.0580 | 5.19e-05 | +++ | 0.2273111 | 1.0000000 | chr1 | 34629175 | CSMD2 | Body |
| 18568 | cg01117452 | -0.1664 | 0.0412 | 5.27e-05 | — | 0.2273111 | 1.0000000 | chr14 | 72703626 | RGS6 | Body |
| 307232 | cg22153116 | 0.1627 | 0.0402 | 5.30e-05 | -++ | 0.2273111 | 1.0000000 | chr9 | 15306736 | TTC39B;TTC39B;TTC39B;TTC39B | Body;Body;Body;Body |
| 351351 | cg25687423 | -0.1654 | 0.0412 | 5.82e-05 | — | 0.2419608 | 1.0000000 | chr6 | 43193521 | C6orf108;C6orf108 | Body;3’UTR |
| 301289 | cg21629895 | -0.1786 | 0.0444 | 5.82e-05 | — | 0.2419608 | 1.0000000 | chr2 | 25565795 | DNMT3A;DNMT3A;DNMT3A | TSS1500;TSS1500;TSS1500 |
| 153656 | cg10308749 | -0.3923 | 0.0976 | 5.84e-05 | — | 0.2419608 | 1.0000000 | chr6 | 126080335 | HEY2 | Body |
| 199878 | cg13797073 | -0.2046 | 0.0509 | 5.93e-05 | — | 0.2431043 | 1.0000000 | chr9 | 71199964 | ||
| 139515 | cg09275980 | 0.3030 | 0.0755 | 6.04e-05 | +++ | 0.2449941 | 1.0000000 | chr15 | 25350925 | SNORD116-29 | TSS1500 |
| 184603 | cg12673019 | -0.1488 | 0.0371 | 6.12e-05 | +– | 0.2458402 | 1.0000000 | chr11 | 17939679 | SERGEF | Body |
| 100076 | cg06555468 | 0.2055 | 0.0514 | 6.28e-05 | +++ | 0.2481358 | 1.0000000 | chr7 | 2094790 | MAD1L1;MAD1L1;MAD1L1 | Body;Body;Body |
| 309222 | cg22332910 | 0.2330 | 0.0582 | 6.34e-05 | +++ | 0.2481358 | 1.0000000 | chr11 | 35641226 | FJX1 | 1stExon |
| 157910 | cg10615519 | 0.4241 | 0.1061 | 6.42e-05 | +++ | 0.2481358 | 1.0000000 | chr12 | 88974243 | KITLG;KITLG | TSS200;TSS200 |
| 116539 | cg07636145 | -0.2033 | 0.0509 | 6.45e-05 | — | 0.2481358 | 1.0000000 | chr16 | 56228188 | DKFZP434H168;GNAO1;GNAO1 | Body;Body;Body |
| 131348 | cg08680083 | -0.2311 | 0.0579 | 6.64e-05 | — | 0.2481358 | 1.0000000 | chr19 | 50309143 | AP2A1;AP2A1 | Body;Body |
| 16383 | cg00990385 | -0.1788 | 0.0448 | 6.70e-05 | — | 0.2481358 | 1.0000000 | chr12 | 113587690 | CCDC42B | 1stExon |
| X | ONTOLOGY | TERM | N | DE | P.DE | FDR | SigGenesInSet |
|---|---|---|---|---|---|---|---|
| GO:0000132 | BP | establishment of mitotic spindle orientation | 30 | 1 | 0.0170717 | 1 | SPRY1 |
| GO:0000578 | BP | embryonic axis specification | 36 | 1 | 0.0241637 | 1 | WNT5A |
| GO:0000932 | CC | P-body | 86 | 1 | 0.0416833 | 1 | RBPMS |
| GO:0001654 | BP | eye development | 373 | 2 | 0.0283476 | 1 | SPRY1,WNT5A |
| GO:0001655 | BP | urogenital system development | 320 | 2 | 0.0204470 | 1 | SPRY1,WNT5A |
| GO:0001702 | BP | gastrulation with mouth forming second | 26 | 1 | 0.0205125 | 1 | WNT5A |
| GO:0001708 | BP | cell fate specification | 99 | 2 | 0.0032883 | 1 | OLIG3,WNT5A |
| GO:0001756 | BP | somitogenesis | 67 | 1 | 0.0478998 | 1 | WNT5A |
| GO:0001759 | BP | organ induction | 23 | 2 | 0.0002145 | 1 | SPRY1,WNT5A |
| GO:0001763 | BP | morphogenesis of a branching structure | 195 | 2 | 0.0110409 | 1 | SPRY1,WNT5A |
| GO:0001837 | BP | epithelial to mesenchymal transition | 147 | 2 | 0.0044294 | 1 | SPRY1,WNT5A |
| GO:0001932 | BP | regulation of protein phosphorylation | 1405 | 3 | 0.0316030 | 1 | SPRY1,RBPMS,WNT5A |
| GO:0001947 | BP | heart looping | 62 | 1 | 0.0402549 | 1 | WNT5A |
| GO:0001961 | BP | positive regulation of cytokine-mediated signaling pathway | 49 | 1 | 0.0147355 | 1 | WNT5A |
| GO:0002011 | BP | morphogenesis of an epithelial sheet | 56 | 1 | 0.0451227 | 1 | WNT5A |
| GO:0002053 | BP | positive regulation of mesenchymal cell proliferation | 25 | 1 | 0.0307164 | 1 | WNT5A |
| GO:0002066 | BP | columnar/cuboidal epithelial cell development | 62 | 1 | 0.0434813 | 1 | WNT5A |
| GO:0002067 | BP | glandular epithelial cell differentiation | 48 | 1 | 0.0425664 | 1 | WNT5A |
| GO:0002068 | BP | glandular epithelial cell development | 26 | 1 | 0.0248938 | 1 | WNT5A |
| GO:0002072 | BP | optic cup morphogenesis involved in camera-type eye development | 8 | 1 | 0.0105911 | 1 | WNT5A |
| GO:0002088 | BP | lens development in camera-type eye | 80 | 2 | 0.0011900 | 1 | SPRY1,WNT5A |
| GO:0002367 | BP | cytokine production involved in immune response | 94 | 1 | 0.0371153 | 1 | WNT5A |
| GO:0002687 | BP | positive regulation of leukocyte migration | 131 | 1 | 0.0435196 | 1 | WNT5A |
| GO:0002688 | BP | regulation of leukocyte chemotaxis | 112 | 1 | 0.0390771 | 1 | WNT5A |
| GO:0002690 | BP | positive regulation of leukocyte chemotaxis | 89 | 1 | 0.0297444 | 1 | WNT5A |
| GO:0002700 | BP | regulation of production of molecular mediator of immune response | 130 | 1 | 0.0466534 | 1 | WNT5A |
| GO:0002702 | BP | positive regulation of production of molecular mediator of immune response | 93 | 1 | 0.0320167 | 1 | WNT5A |
| GO:0002718 | BP | regulation of cytokine production involved in immune response | 74 | 1 | 0.0341841 | 1 | WNT5A |
| GO:0002720 | BP | positive regulation of cytokine production involved in immune response | 50 | 1 | 0.0216393 | 1 | WNT5A |
| GO:0003002 | BP | regionalization | 343 | 2 | 0.0280862 | 1 | SPRY1,WNT5A |
| GO:0003007 | BP | heart morphogenesis | 255 | 2 | 0.0147387 | 1 | SPRY1,WNT5A |
| GO:0003128 | BP | heart field specification | 17 | 1 | 0.0197641 | 1 | WNT5A |
| GO:0003129 | BP | heart induction | 10 | 1 | 0.0112860 | 1 | WNT5A |
| GO:0003138 | BP | primary heart field specification | 3 | 1 | 0.0039931 | 1 | WNT5A |
| GO:0003139 | BP | secondary heart field specification | 11 | 1 | 0.0124197 | 1 | WNT5A |
| GO:0003143 | BP | embryonic heart tube morphogenesis | 68 | 1 | 0.0462131 | 1 | WNT5A |
| GO:0003156 | BP | regulation of animal organ formation | 37 | 2 | 0.0006690 | 1 | SPRY1,WNT5A |
| GO:0003209 | BP | cardiac atrium morphogenesis | 30 | 1 | 0.0274007 | 1 | WNT5A |
| GO:0003213 | BP | cardiac right atrium morphogenesis | 2 | 1 | 0.0041147 | 1 | WNT5A |
| GO:0003230 | BP | cardiac atrium development | 36 | 1 | 0.0298481 | 1 | WNT5A |
| GO:0003283 | BP | atrial septum development | 23 | 1 | 0.0203575 | 1 | WNT5A |
| GO:0003306 | BP | Wnt signaling pathway involved in heart development | 13 | 1 | 0.0077832 | 1 | WNT5A |
| GO:0003307 | BP | regulation of Wnt signaling pathway involved in heart development | 9 | 1 | 0.0048594 | 1 | WNT5A |
| GO:0003308 | BP | negative regulation of Wnt signaling pathway involved in heart development | 7 | 1 | 0.0033385 | 1 | WNT5A |
| GO:0003309 | BP | type B pancreatic cell differentiation | 25 | 1 | 0.0221791 | 1 | WNT5A |
| GO:0003323 | BP | type B pancreatic cell development | 20 | 1 | 0.0159645 | 1 | WNT5A |
| GO:0003344 | BP | pericardium morphogenesis | 9 | 1 | 0.0086510 | 1 | WNT5A |
| GO:0003401 | BP | axis elongation | 28 | 2 | 0.0003656 | 1 | SPRY1,WNT5A |
| GO:0003402 | BP | planar cell polarity pathway involved in axis elongation | 6 | 1 | 0.0093298 | 1 | WNT5A |
| GO:0003408 | BP | optic cup formation involved in camera-type eye development | 3 | 1 | 0.0040144 | 1 | WNT5A |
| GO:0003712 | MF | transcription coregulator activity | 462 | 2 | 0.0239655 | 1 | RBPMS,OLIG3 |
| GO:0003727 | MF | single-stranded RNA binding | 81 | 1 | 0.0376670 | 1 | RBPMS |
| GO:0003729 | MF | mRNA binding | 491 | 2 | 0.0054702 | 1 | RBPMS,SRRM2 |
| GO:0005109 | MF | frizzled binding | 37 | 1 | 0.0306569 | 1 | WNT5A |
| GO:0005115 | MF | receptor tyrosine kinase-like orphan receptor binding | 1 | 1 | 0.0020187 | 1 | WNT5A |
| GO:0005543 | MF | phospholipid binding | 425 | 2 | 0.0226882 | 1 | MCF2L,WNT5A |
| GO:0005681 | CC | spliceosomal complex | 177 | 1 | 0.0442644 | 1 | SRRM2 |
| GO:0005684 | CC | U2-type spliceosomal complex | 88 | 1 | 0.0244405 | 1 | SRRM2 |
| GO:0006139 | BP | nucleobase-containing compound metabolic process | 5578 | 5 | 0.0385323 | 1 | RBPMS,OLIG3,SRRM2,WNT5A,PPT2 |
| GO:0006396 | BP | RNA processing | 1235 | 2 | 0.0261175 | 1 | RBPMS,SRRM2 |
| GO:0006582 | BP | melanin metabolic process | 22 | 1 | 0.0137342 | 1 | WNT5A |
| GO:0006637 | BP | acyl-CoA metabolic process | 95 | 1 | 0.0343804 | 1 | PPT2 |
| GO:0006725 | BP | cellular aromatic compound metabolic process | 5786 | 5 | 0.0436372 | 1 | RBPMS,OLIG3,SRRM2,WNT5A,PPT2 |
| GO:0006793 | BP | phosphorus metabolic process | 3152 | 4 | 0.0465551 | 1 | SPRY1,RBPMS,WNT5A,PPT2 |
| GO:0006796 | BP | phosphate-containing compound metabolic process | 3127 | 4 | 0.0453948 | 1 | SPRY1,RBPMS,WNT5A,PPT2 |
| GO:0007163 | BP | establishment or maintenance of cell polarity | 214 | 2 | 0.0091182 | 1 | SPRY1,WNT5A |
| GO:0007167 | BP | enzyme linked receptor protein signaling pathway | 1029 | 3 | 0.0217499 | 1 | SPRY1,RBPMS,WNT5A |
| GO:0007178 | BP | transmembrane receptor protein serine/threonine kinase signaling pathway | 341 | 3 | 0.0012016 | 1 | SPRY1,RBPMS,WNT5A |
| GO:0007223 | BP | Wnt signaling pathway, calcium modulating pathway | 38 | 1 | 0.0289937 | 1 | WNT5A |
| GO:0007257 | BP | activation of JUN kinase activity | 38 | 1 | 0.0243513 | 1 | WNT5A |
| GO:0007264 | BP | small GTPase mediated signal transduction | 469 | 2 | 0.0393178 | 1 | SPRY1,MCF2L |
| GO:0007350 | BP | blastoderm segmentation | 20 | 1 | 0.0186601 | 1 | WNT5A |
| GO:0007351 | BP | tripartite regional subdivision | 16 | 1 | 0.0140401 | 1 | WNT5A |
| GO:0007389 | BP | pattern specification process | 436 | 2 | 0.0405926 | 1 | SPRY1,WNT5A |
| GO:0007442 | BP | hindgut morphogenesis | 7 | 1 | 0.0094349 | 1 | WNT5A |
| GO:0007494 | BP | midgut development | 12 | 1 | 0.0125057 | 1 | WNT5A |
| GO:0008143 | MF | poly(A) binding | 21 | 1 | 0.0095053 | 1 | RBPMS |
| GO:0008474 | MF | palmitoyl-(protein) hydrolase activity | 13 | 1 | 0.0047432 | 1 | PPT2 |
| GO:0008543 | BP | fibroblast growth factor receptor signaling pathway | 112 | 2 | 0.0021005 | 1 | SPRY1,WNT5A |
| GO:0008595 | BP | anterior/posterior axis specification, embryo | 16 | 1 | 0.0140401 | 1 | WNT5A |
| GO:0009948 | BP | anterior/posterior axis specification | 48 | 1 | 0.0317891 | 1 | WNT5A |
| GO:0010092 | BP | specification of animal organ identity | 35 | 2 | 0.0006903 | 1 | SPRY1,WNT5A |
| GO:0010453 | BP | regulation of cell fate commitment | 37 | 1 | 0.0217979 | 1 | WNT5A |
| GO:0010463 | BP | mesenchymal cell proliferation | 43 | 1 | 0.0467404 | 1 | WNT5A |
| GO:0010464 | BP | regulation of mesenchymal cell proliferation | 33 | 1 | 0.0385379 | 1 | WNT5A |
| GO:0010494 | CC | cytoplasmic stress granule | 69 | 1 | 0.0263234 | 1 | RBPMS |
| GO:0010719 | BP | negative regulation of epithelial to mesenchymal transition | 40 | 1 | 0.0284573 | 1 | SPRY1 |
| GO:0010799 | BP | regulation of peptidyl-threonine phosphorylation | 46 | 1 | 0.0307112 | 1 | WNT5A |
| GO:0010800 | BP | positive regulation of peptidyl-threonine phosphorylation | 28 | 1 | 0.0185498 | 1 | WNT5A |
| GO:0010818 | BP | T cell chemotaxis | 22 | 1 | 0.0071995 | 1 | WNT5A |
| GO:0010819 | BP | regulation of T cell chemotaxis | 15 | 1 | 0.0049580 | 1 | WNT5A |
| GO:0010820 | BP | positive regulation of T cell chemotaxis | 14 | 1 | 0.0049580 | 1 | WNT5A |
| GO:0010862 | BP | positive regulation of pathway-restricted SMAD protein phosphorylation | 47 | 1 | 0.0192732 | 1 | RBPMS |
| GO:0010934 | BP | macrophage cytokine production | 15 | 1 | 0.0081533 | 1 | WNT5A |
| GO:0010935 | BP | regulation of macrophage cytokine production | 14 | 1 | 0.0078638 | 1 | WNT5A |
| GO:0015030 | CC | Cajal body | 70 | 1 | 0.0124663 | 1 | SRRM2 |
| GO:0016790 | MF | thiolester hydrolase activity | 38 | 1 | 0.0128339 | 1 | PPT2 |
| GO:0019748 | BP | secondary metabolic process | 55 | 1 | 0.0252502 | 1 | WNT5A |
| GO:0021517 | BP | ventral spinal cord development | 48 | 1 | 0.0444256 | 1 | OLIG3 |
| GO:0021520 | BP | spinal cord motor neuron cell fate specification | 13 | 1 | 0.0173372 | 1 | OLIG3 |
metal_all_cell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/all_cell_common_1204201.tbl', sep = "\t")
metal_all_cell = metalProcess(metal_all_cell)
write.csv(metal_all_cell, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DMP_all_cell_common_120420.csv')
# Significant probes
# Nominal P-value
table(metal_all_cell$P.value < 0.05)
# FALSE TRUE
# 354739 22612
# FDR
table(metal_all_cell$P.FDR < 0.05)
# FALSE TRUE
# 377348 3
table(metal_all_cell$P.FDR < 0.1)
# FALSE TRUE
# 377326 25
# Bonferroni
table(metal_all_cell$P.Bonf < 0.05)
# FALSE
# 377351
# GO analysis, nominally-significant probes
go_metal_all_cell = gometh(sig.cpg = metal_all_cell$Name[metal_all_cell$P.FDR < 0.1], all.cpg = metal_all_cell$Name, array.type = '450K', anno = annAll2)
go_metal_all_cell = go_metal_all_cell[order(go_metal_all_cell$P.DE),]
table(go_metal_all_cell$P.DE<0.05)
# FALSE TRUE
# 22246 337
table(go_metal_all_cell$FDR<0.05)
# FALSE
# 22583
write.csv(go_metal_all_cell[go_metal_all_cell$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DMP_all_cell_common_120420.csv')
# KEGG analysis, nominally-significant probes
kegg_metal_all_cell = gometh(sig.cpg = metal_all_cell$Name[metal_all_cell$P.FDR < 0.1], all.cpg = metal_all_cell$Name, array.type = '450K', collection = 'KEGG', sig.genes = T, anno = annAll2)
kegg_metal_all_cell = kegg_metal_all_cell[order(kegg_metal_all_cell$P.DE),]
table(kegg_metal_all_cell$P.DE<0.05)
# FALSE TRUE
# 335 5
table(kegg_metal_all_cell$FDR<0.05)
# FALSE
# 340
write.csv(kegg_metal_all_cell[c(1:20),], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DMP_all_cell_common_120420.csv')
# Plotting
gg_qqplot(metal_all_cell$P.value)
quartz.save('qq_metal_all_cell_120420.png', type = "png", dpi = 300)
manhattan_meta(metal_all_cell, FDR=T)
quartz.save('manhattan_metal_all_cell_120420.png', type = "png", dpi = 300)
volcano_meta(metal_all_cell)
quartz.save('volcano_metal_all_cell_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_all_cell_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_all_cell_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_all_cell_120420.png")
| X | Name | Effect | StdErr | P.value | Direction | P.FDR | P.Bonf | chr | pos | UCSC_RefGene_Name | UCSC_RefGene_Group |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 139515 | cg09275980 | 0.3064 | 0.0594 | 3.00e-07 | ++++ | 0.0415715 | 0.0950925 | chr15 | 25350925 | SNORD116-29 | TSS1500 |
| 291217 | cg20784693 | -0.6410 | 0.1252 | 3.00e-07 | —- | 0.0415715 | 0.1162996 | chr2 | 239984030 | HDAC4 | Body |
| 260100 | cg18263451 | -0.1213 | 0.0238 | 3.00e-07 | –+- | 0.0415715 | 0.1247145 | chr1 | 25573180 | C1orf63 | Body |
| 254158 | cg17819053 | 0.1723 | 0.0348 | 7.00e-07 | ++++ | 0.0603460 | 0.2826736 | chr1 | 119549626 | ||
| 95521 | cg06218338 | 0.3110 | 0.0630 | 8.00e-07 | -+++ | 0.0603460 | 0.3017299 | chr7 | 27231894 | ||
| 284743 | cg20247661 | 0.1739 | 0.0356 | 1.00e-06 | -+++ | 0.0633950 | 0.3890489 | chr10 | 21812368 | C10orf140 | 5’UTR |
| 184123 | cg12637057 | 0.2531 | 0.0521 | 1.20e-06 | ++++ | 0.0633950 | 0.4437648 | chr20 | 59967284 | CDH4 | Body |
| 46686 | cg02925222 | 0.1166 | 0.0242 | 1.40e-06 | ++++ | 0.0637723 | 0.5305555 | chr11 | 280445 | NLRP6 | Body |
| 90057 | cg05837401 | 0.2379 | 0.0496 | 1.60e-06 | ++++ | 0.0637723 | 0.6052710 | chr3 | 125899086 | ALDH1L1 | 5’UTR |
| 222521 | cg15345437 | -0.1530 | 0.0320 | 1.70e-06 | —- | 0.0637723 | 0.6377232 | chr11 | 62620843 | SNORD22;SNORD31;SNHG1 | TSS1500;Body;Body |
| 114412 | cg07492924 | -0.3734 | 0.0791 | 2.40e-06 | —- | 0.0810276 | 0.8913031 | chr16 | 433825 | LOC100134368 | Body |
| 143925 | cg09595163 | 0.4584 | 0.0977 | 2.70e-06 | +++- | 0.0832204 | 1.0000000 | chr3 | 55515541 | WNT5A | Body |
| 44706 | cg02799448 | 0.1600 | 0.0342 | 2.90e-06 | -++- | 0.0832204 | 1.0000000 | chr6 | 137817008 | OLIG3 | TSS1500 |
| 194923 | cg13490635 | 0.2316 | 0.0500 | 3.50e-06 | +++- | 0.0931114 | 1.0000000 | chr8 | 30242021 | RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS | 5’UTR;5’UTR;1stExon;1stExon;1stExon;5’UTR;1stExon;5’UTR |
| 225228 | cg15572907 | 0.5107 | 0.1105 | 3.80e-06 | ++++ | 0.0931114 | 1.0000000 | chr19 | 40995921 | SPTBN4 | Body |
| 9270 | cg00550554 | -0.1879 | 0.0407 | 3.90e-06 | —- | 0.0931114 | 1.0000000 | chr6 | 30294969 | HCG18;TRIM39;HCG18;TRIM39 | TSS200;5’UTR;TSS200;TSS200 |
| 138010 | cg09169455 | -0.4663 | 0.1015 | 4.30e-06 | —- | 0.0953755 | 1.0000000 | chr5 | 16843340 | MYO10 | Body |
| 360597 | cg26412543 | -0.2220 | 0.0485 | 4.70e-06 | —- | 0.0953755 | 1.0000000 | chr6 | 32128829 | PPT2;PPT2 | Body;Body |
| 363371 | cg26623444 | 0.1849 | 0.0406 | 5.10e-06 | ++++ | 0.0953755 | 1.0000000 | chr7 | 31376092 | ||
| 30961 | cg01927825 | -0.2978 | 0.0654 | 5.30e-06 | —- | 0.0953755 | 1.0000000 | chr1 | 2121724 | C1orf86;LOC100128003;C1orf86 | Body;Body;Body |
| 343981 | cg25076597 | -0.3140 | 0.0690 | 5.40e-06 | —- | 0.0953755 | 1.0000000 | chr10 | 134150581 | LRRC27;LRRC27;LRRC27;LRRC27;LRRC27 | Body;TSS200;Body;Body;Body |
| 23933 | cg01464730 | -0.7679 | 0.1692 | 5.60e-06 | —- | 0.0953755 | 1.0000000 | chr17 | 78809873 | RPTOR;RPTOR | Body;Body |
| 136234 | cg09035938 | 0.1847 | 0.0408 | 6.00e-06 | ++++ | 0.0953755 | 1.0000000 | chr1 | 35347799 | DLGAP3 | Body |
| 33505 | cg02081266 | 0.3474 | 0.0768 | 6.10e-06 | ++++ | 0.0953755 | 1.0000000 | chr17 | 59529618 | ||
| 277060 | cg19640581 | -0.2875 | 0.0638 | 6.50e-06 | —- | 0.0977943 | 1.0000000 | chr5 | 501343 | SLC9A3 | Body |
| 61580 | cg03906434 | 0.3385 | 0.0755 | 7.30e-06 | -+++ | 0.1050131 | 1.0000000 | chr7 | 27231819 | ||
| 299146 | cg21468180 | -0.1345 | 0.0301 | 7.80e-06 | —- | 0.1050131 | 1.0000000 | chr3 | 13697288 | LOC285375 | Body |
| 243179 | cg16919449 | -0.4103 | 0.0919 | 8.10e-06 | —- | 0.1050131 | 1.0000000 | chr10 | 36054185 | ||
| 373928 | cg27406919 | -0.1775 | 0.0399 | 8.50e-06 | —- | 0.1050131 | 1.0000000 | chr16 | 87212733 | ||
| 41431 | cg02591871 | -0.1270 | 0.0285 | 8.60e-06 | —- | 0.1050131 | 1.0000000 | chr19 | 14228565 | PRKACA | TSS200 |
| 187357 | cg12908187 | 0.1860 | 0.0418 | 8.60e-06 | -+++ | 0.1050131 | 1.0000000 | chr16 | 88450261 | ||
| 119415 | cg07840143 | 0.1625 | 0.0372 | 1.24e-05 | ++++ | 0.1438508 | 1.0000000 | chr5 | 3324860 | ||
| 56100 | cg03544320 | 0.3008 | 0.0689 | 1.26e-05 | -+++ | 0.1438508 | 1.0000000 | chr4 | 5894691 | CRMP1 | 1stExon |
| 330881 | cg24053992 | 0.1754 | 0.0403 | 1.38e-05 | +-++ | 0.1468524 | 1.0000000 | chr1 | 119554564 | ||
| 197997 | cg13677022 | -0.1546 | 0.0356 | 1.39e-05 | —- | 0.1468524 | 1.0000000 | chr9 | 34625963 | ARID3C | Body |
| 35348 | cg02206980 | -0.4156 | 0.0957 | 1.40e-05 | —- | 0.1468524 | 1.0000000 | chr6 | 13574034 | SIRT5;SIRT5 | TSS1500;TSS1500 |
| 240943 | cg16734734 | 0.1558 | 0.0360 | 1.52e-05 | –++ | 0.1545099 | 1.0000000 | chr6 | 105624309 | POPDC3;POPDC3 | TSS200;5’UTR |
| 64145 | cg04080022 | -0.1761 | 0.0409 | 1.66e-05 | —+ | 0.1646442 | 1.0000000 | chr16 | 89648534 | CPNE7;CPNE7 | Body;Body |
| 237459 | cg16502049 | -0.0984 | 0.0229 | 1.71e-05 | —- | 0.1648080 | 1.0000000 | chr20 | 23402203 | NAPB | TSS200 |
| 218644 | cg15025362 | 0.1569 | 0.0365 | 1.75e-05 | ++-+ | 0.1648080 | 1.0000000 | chr3 | 186256331 | CRYGS | 3’UTR |
| 113100 | cg07399977 | -0.1659 | 0.0387 | 1.82e-05 | —- | 0.1679212 | 1.0000000 | chr1 | 27339612 | FAM46B | TSS1500 |
| 301289 | cg21629895 | -0.1761 | 0.0412 | 1.88e-05 | —- | 0.1679212 | 1.0000000 | chr2 | 25565795 | DNMT3A;DNMT3A;DNMT3A | TSS1500;TSS1500;TSS1500 |
| 58832 | cg03720762 | -0.2458 | 0.0576 | 1.96e-05 | —- | 0.1679212 | 1.0000000 | chr17 | 17604184 | RAI1 | 5’UTR |
| 168281 | cg11414610 | -0.1279 | 0.0300 | 1.96e-05 | —- | 0.1679212 | 1.0000000 | chr19 | 16528319 | EPS15L1 | Body |
| 176796 | cg12065616 | -0.1588 | 0.0373 | 2.03e-05 | —- | 0.1700595 | 1.0000000 | chr12 | 94954828 | ||
| 6030 | cg00358880 | 0.1679 | 0.0395 | 2.16e-05 | ++++ | 0.1768628 | 1.0000000 | chr1 | 197885105 | LHX9;LHX9 | TSS1500;Body |
| 191691 | cg13278267 | 0.1750 | 0.0414 | 2.36e-05 | ++++ | 0.1847510 | 1.0000000 | chr2 | 38742843 | ||
| 21418 | cg01303372 | -0.1905 | 0.0451 | 2.43e-05 | —- | 0.1847510 | 1.0000000 | chr10 | 121415189 | BAG3 | Body |
| 228619 | cg15830431 | 0.1587 | 0.0376 | 2.43e-05 | ++-+ | 0.1847510 | 1.0000000 | chr8 | 99952591 | ||
| 150668 | cg10098010 | 0.2199 | 0.0521 | 2.45e-05 | ++++ | 0.1847510 | 1.0000000 | chr6 | 138483709 | KIAA1244 | Body |
| 34800 | cg02166532 | 0.1646 | 0.0392 | 2.61e-05 | ++++ | 0.1883103 | 1.0000000 | chr11 | 2159853 | INS-IGF2;IGF2;IGF2;IGF2;IGF2 | Body;Body;5’UTR;5’UTR;1stExon |
| 91398 | cg05926253 | 0.1388 | 0.0331 | 2.70e-05 | -+++ | 0.1883103 | 1.0000000 | chr5 | 1801364 | NDUFS6;MRPL36 | TSS200;TSS1500 |
| 196894 | cg13609065 | 0.0857 | 0.0204 | 2.72e-05 | -+++ | 0.1883103 | 1.0000000 | chr17 | 6613894 | SLC13A5;SLC13A5 | Body;Body |
| 356139 | cg26090406 | 0.2617 | 0.0624 | 2.76e-05 | ++++ | 0.1883103 | 1.0000000 | chr13 | 110937644 | COL4A1 | Body |
| 50150 | cg03149958 | -0.1704 | 0.0408 | 2.91e-05 | —- | 0.1883103 | 1.0000000 | chr6 | 36326677 | ||
| 5363 | cg00321074 | -0.1267 | 0.0303 | 2.92e-05 | —- | 0.1883103 | 1.0000000 | chr3 | 19990693 | RAB5A | 5’UTR |
| 331853 | cg24127593 | 0.1811 | 0.0433 | 2.95e-05 | ++++ | 0.1883103 | 1.0000000 | chr4 | 1648399 | FAM53A | Body |
| 48278 | cg03025061 | -0.1653 | 0.0396 | 2.96e-05 | —- | 0.1883103 | 1.0000000 | chr8 | 109261275 | EIF3E | TSS1500 |
| 33761 | cg02097144 | 0.1717 | 0.0411 | 2.99e-05 | +-++ | 0.1883103 | 1.0000000 | chr7 | 78280216 | MAGI2 | Body |
| 117587 | cg07712198 | 0.1970 | 0.0472 | 3.04e-05 | -+++ | 0.1883103 | 1.0000000 | chr5 | 9015582 | ||
| 93 | cg00004257 | 0.2233 | 0.0536 | 3.06e-05 | ++++ | 0.1883103 | 1.0000000 | chr1 | 34629175 | CSMD2 | Body |
| 180441 | cg12354986 | -0.1980 | 0.0475 | 3.09e-05 | +— | 0.1883103 | 1.0000000 | chr22 | 38142174 | TRIOBP;TRIOBP;TRIOBP | TSS200;Body;TSS200 |
| 136896 | cg09088406 | 0.2510 | 0.0603 | 3.17e-05 | ++++ | 0.1900531 | 1.0000000 | chr15 | 27819306 | ||
| 323848 | cg23504707 | 0.1527 | 0.0367 | 3.24e-05 | ++++ | 0.1904752 | 1.0000000 | chr14 | 60712563 | PPM1A;PPM1A | 5’UTR;1stExon |
| 80941 | cg05197323 | -0.1184 | 0.0285 | 3.28e-05 | +— | 0.1904752 | 1.0000000 | chr14 | 24912098 | SDR39U1 | TSS200 |
| 351351 | cg25687423 | -0.1619 | 0.0391 | 3.47e-05 | —- | 0.1983951 | 1.0000000 | chr6 | 43193521 | C6orf108;C6orf108 | Body;3’UTR |
| 218811 | cg15035705 | -0.1756 | 0.0425 | 3.67e-05 | —- | 0.2050633 | 1.0000000 | chr5 | 179159291 | MAML1 | TSS1500 |
| 166619 | cg11289100 | 0.2128 | 0.0516 | 3.75e-05 | ++++ | 0.2050633 | 1.0000000 | chr17 | 19313024 | RNF112 | TSS1500 |
| 325843 | cg23662713 | 0.2955 | 0.0717 | 3.75e-05 | ++++ | 0.2050633 | 1.0000000 | chr14 | 36741645 | ||
| 217427 | cg14931071 | 0.1339 | 0.0325 | 3.80e-05 | —+ | 0.2050633 | 1.0000000 | chr6 | 12717776 | PHACTR1 | TSS200 |
| 316250 | cg22915154 | -0.2026 | 0.0493 | 3.95e-05 | —- | 0.2100410 | 1.0000000 | chr11 | 68816030 | TPCN2 | TSS1500 |
| 247434 | cg17260318 | -0.1813 | 0.0442 | 4.04e-05 | —- | 0.2118407 | 1.0000000 | chr19 | 4067604 | ZBTB7A | TSS1500 |
| 86700 | cg05595134 | 0.3324 | 0.0811 | 4.18e-05 | +-++ | 0.2140702 | 1.0000000 | chr8 | 55047255 | MRPL15 | TSS1500 |
| 292390 | cg20899625 | -0.1360 | 0.0332 | 4.20e-05 | —- | 0.2140702 | 1.0000000 | chr3 | 126721131 | PLXNA1 | Body |
| 352336 | cg25763542 | -0.2870 | 0.0702 | 4.36e-05 | —- | 0.2160684 | 1.0000000 | chr19 | 310512 | MIER2 | Body |
| 20130 | cg01218206 | -0.1738 | 0.0426 | 4.44e-05 | —+ | 0.2160684 | 1.0000000 | chr11 | 116933977 | SIK3 | Body |
| 173650 | cg11831006 | -0.1901 | 0.0466 | 4.49e-05 | —- | 0.2160684 | 1.0000000 | chr3 | 125100635 | ||
| 307701 | cg22193385 | -0.1780 | 0.0436 | 4.52e-05 | –+- | 0.2160684 | 1.0000000 | chr12 | 52638005 | KRT7 | Body |
| 304218 | cg21885638 | -0.1256 | 0.0308 | 4.53e-05 | —- | 0.2160684 | 1.0000000 | chr3 | 129306552 | PLXND1 | Body |
| 324549 | cg23558842 | 0.2833 | 0.0695 | 4.59e-05 | ++++ | 0.2160684 | 1.0000000 | chr11 | 15095178 | CALCB;CALCB | 1stExon;5’UTR |
| 73455 | cg04696969 | 0.2340 | 0.0574 | 4.64e-05 | ++++ | 0.2160684 | 1.0000000 | chr2 | 223335429 | SGPP2 | Body |
| 233115 | cg16188243 | -0.2292 | 0.0564 | 4.79e-05 | —- | 0.2192273 | 1.0000000 | chr19 | 2783719 | SGTA | TSS1500 |
| 30412 | cg01892516 | 0.4813 | 0.1184 | 4.82e-05 | ++++ | 0.2192273 | 1.0000000 | chr14 | 38064532 | FOXA1 | TSS200 |
| 168526 | cg11434671 | -0.1410 | 0.0347 | 4.92e-05 | —- | 0.2198846 | 1.0000000 | chr17 | 74524611 | CYGB | 3’UTR |
| 222274 | cg15323873 | -0.1523 | 0.0375 | 4.95e-05 | —- | 0.2198846 | 1.0000000 | chr10 | 79650526 | DLG5 | Body |
| 168429 | cg11425470 | -0.1704 | 0.0420 | 5.06e-05 | —- | 0.2221106 | 1.0000000 | chr1 | 109271795 | FNDC7 | Body |
| 17916 | cg01078824 | 0.1416 | 0.0350 | 5.13e-05 | ++++ | 0.2224636 | 1.0000000 | chr7 | 27220047 | HOXA10 | TSS200 |
| 219413 | cg15083775 | 0.1294 | 0.0320 | 5.25e-05 | –++ | 0.2244178 | 1.0000000 | chr17 | 48054048 | ||
| 228483 | cg15822394 | -0.1875 | 0.0464 | 5.29e-05 | —- | 0.2244178 | 1.0000000 | chr19 | 17877733 | FCHO1;FCHO1;FCHO1;FCHO1 | Body;Body;Body;Body |
| 162133 | cg10945313 | 0.1774 | 0.0440 | 5.50e-05 | ++++ | 0.2306034 | 1.0000000 | chr4 | 113739291 | ANK2;ANK2 | 5’UTR;1stExon |
| 223845 | cg15454856 | 0.0991 | 0.0246 | 5.76e-05 | ++-+ | 0.2389337 | 1.0000000 | chr7 | 108168130 | PNPLA8 | TSS1500 |
| 225048 | cg15557168 | 0.4852 | 0.1208 | 5.90e-05 | +-++ | 0.2414276 | 1.0000000 | chr22 | 42548783 | ||
| 275492 | cg19519624 | -0.2199 | 0.0548 | 5.96e-05 | —- | 0.2414276 | 1.0000000 | chr9 | 138881792 | ||
| 192044 | cg13305951 | -0.2022 | 0.0504 | 6.10e-05 | —- | 0.2414276 | 1.0000000 | chr17 | 19314618 | RNF112;RNF112 | 1stExon;5’UTR |
| 330819 | cg24049616 | 0.1591 | 0.0397 | 6.22e-05 | ++++ | 0.2414276 | 1.0000000 | chr16 | 55359029 | IRX6 | 1stExon |
| 358903 | cg26290114 | -0.1633 | 0.0408 | 6.22e-05 | —- | 0.2414276 | 1.0000000 | chr13 | 52159332 | WDFY2 | Body |
| 174808 | cg11914514 | -0.1747 | 0.0437 | 6.27e-05 | —- | 0.2414276 | 1.0000000 | chr9 | 131218865 | ODF2;ODF2 | TSS1500;5’UTR |
| 279041 | cg19784205 | -0.2088 | 0.0522 | 6.27e-05 | —- | 0.2414276 | 1.0000000 | chr12 | 132473879 | EP400 | Body |
| 34418 | cg02141929 | -0.1944 | 0.0486 | 6.38e-05 | —- | 0.2432580 | 1.0000000 | chr16 | 56681544 | ||
| 134866 | cg08928966 | 0.1305 | 0.0327 | 6.58e-05 | +-++ | 0.2459133 | 1.0000000 | chr3 | 51859710 |
| X | ONTOLOGY | TERM | N | DE | P.DE | FDR |
|---|---|---|---|---|---|---|
| GO:0010800 | BP | positive regulation of peptidyl-threonine phosphorylation | 28 | 2 | 0.0012414 | 1 |
| GO:0033135 | BP | regulation of peptidyl-serine phosphorylation | 125 | 3 | 0.0014291 | 1 |
| GO:0030507 | MF | spectrin binding | 28 | 2 | 0.0023516 | 1 |
| GO:0010494 | CC | cytoplasmic stress granule | 69 | 2 | 0.0031785 | 1 |
| GO:0010799 | BP | regulation of peptidyl-threonine phosphorylation | 46 | 2 | 0.0034741 | 1 |
| GO:0005000 | MF | vasopressin receptor activity | 6 | 1 | 0.0035990 | 1 |
| GO:0032535 | BP | regulation of cellular component size | 359 | 4 | 0.0037773 | 1 |
| GO:0009258 | BP | 10-formyltetrahydrofolate catabolic process | 2 | 1 | 0.0039096 | 1 |
| GO:0016155 | MF | formyltetrahydrofolate dehydrogenase activity | 2 | 1 | 0.0039096 | 1 |
| GO:0009397 | BP | folic acid-containing compound catabolic process | 3 | 1 | 0.0042694 | 1 |
| GO:0042560 | BP | pteridine-containing compound catabolic process | 3 | 1 | 0.0042694 | 1 |
| GO:0008361 | BP | regulation of cell size | 169 | 3 | 0.0050394 | 1 |
| GO:0005115 | MF | receptor tyrosine kinase-like orphan receptor binding | 1 | 1 | 0.0052303 | 1 |
| GO:0036517 | BP | chemoattraction of serotonergic neuron axon | 1 | 1 | 0.0052303 | 1 |
| GO:0060599 | BP | lateral sprouting involved in mammary gland duct morphogenesis | 1 | 1 | 0.0052303 | 1 |
| GO:0061347 | BP | planar cell polarity pathway involved in outflow tract morphogenesis | 1 | 1 | 0.0052303 | 1 |
| GO:0061348 | BP | planar cell polarity pathway involved in ventricular septum morphogenesis | 1 | 1 | 0.0052303 | 1 |
| GO:0061349 | BP | planar cell polarity pathway involved in cardiac right atrium morphogenesis | 1 | 1 | 0.0052303 | 1 |
| GO:0061350 | BP | planar cell polarity pathway involved in cardiac muscle tissue morphogenesis | 1 | 1 | 0.0052303 | 1 |
| GO:0061354 | BP | planar cell polarity pathway involved in pericardium morphogenesis | 1 | 1 | 0.0052303 | 1 |
| GO:1904934 | BP | negative regulation of cell proliferation in midbrain | 1 | 1 | 0.0052303 | 1 |
| GO:1904955 | BP | planar cell polarity pathway involved in midbrain dopaminergic neuron differentiation | 1 | 1 | 0.0052303 | 1 |
| GO:0048850 | BP | hypophysis morphogenesis | 2 | 1 | 0.0056017 | 1 |
| GO:1905438 | BP | non-canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation | 2 | 1 | 0.0057409 | 1 |
| GO:0036518 | BP | chemorepulsion of dopaminergic neuron axon | 2 | 1 | 0.0058494 | 1 |
| GO:0051885 | BP | positive regulation of timing of anagen | 2 | 1 | 0.0058573 | 1 |
| GO:0097325 | BP | melanocyte proliferation | 3 | 1 | 0.0059866 | 1 |
| GO:0042695 | BP | thelarche | 3 | 1 | 0.0060342 | 1 |
| GO:0060744 | BP | mammary gland branching involved in thelarche | 3 | 1 | 0.0060342 | 1 |
| GO:0060809 | BP | mesodermal to mesenchymal transition involved in gastrulation | 2 | 1 | 0.0060434 | 1 |
| GO:0060031 | BP | mediolateral intercalation | 2 | 1 | 0.0063463 | 1 |
| GO:0060775 | BP | planar cell polarity pathway involved in gastrula mediolateral intercalation | 2 | 1 | 0.0063463 | 1 |
| GO:0060002 | MF | plus-end directed microfilament motor activity | 3 | 1 | 0.0066603 | 1 |
| GO:1902435 | BP | regulation of male mating behavior | 2 | 1 | 0.0066640 | 1 |
| GO:1902437 | BP | positive regulation of male mating behavior | 2 | 1 | 0.0066640 | 1 |
| GO:1904933 | BP | regulation of cell proliferation in midbrain | 2 | 1 | 0.0073534 | 1 |
| GO:0042640 | BP | anagen | 5 | 1 | 0.0074701 | 1 |
| GO:0051884 | BP | regulation of timing of anagen | 5 | 1 | 0.0074701 | 1 |
| GO:0046543 | BP | development of secondary female sexual characteristics | 5 | 1 | 0.0075654 | 1 |
| GO:0061341 | BP | non-canonical Wnt signaling pathway involved in heart development | 2 | 1 | 0.0077345 | 1 |
| GO:0061346 | BP | planar cell polarity pathway involved in heart morphogenesis | 2 | 1 | 0.0077345 | 1 |
| GO:0090081 | BP | regulation of heart induction by regulation of canonical Wnt signaling pathway | 4 | 1 | 0.0077679 | 1 |
| GO:0090082 | BP | positive regulation of heart induction by negative regulation of canonical Wnt signaling pathway | 4 | 1 | 0.0077679 | 1 |
| GO:0016742 | MF | hydroxymethyl-, formyl- and related transferase activity | 8 | 1 | 0.0078801 | 1 |
| GO:0031594 | CC | neuromuscular junction | 74 | 2 | 0.0082890 | 1 |
| GO:2000243 | BP | positive regulation of reproductive process | 77 | 2 | 0.0083074 | 1 |
| GO:0045136 | BP | development of secondary sexual characteristics | 7 | 1 | 0.0083250 | 1 |
| GO:0048022 | BP | negative regulation of melanin biosynthetic process | 4 | 1 | 0.0086266 | 1 |
| GO:1900377 | BP | negative regulation of secondary metabolite biosynthetic process | 4 | 1 | 0.0086266 | 1 |
| GO:0090066 | BP | regulation of anatomical structure size | 491 | 4 | 0.0090906 | 1 |
| GO:0060762 | BP | regulation of branching involved in mammary gland duct morphogenesis | 4 | 1 | 0.0091396 | 1 |
| GO:0060067 | BP | cervix development | 2 | 1 | 0.0093337 | 1 |
| GO:0003308 | BP | negative regulation of Wnt signaling pathway involved in heart development | 7 | 1 | 0.0094248 | 1 |
| GO:0003408 | BP | optic cup formation involved in camera-type eye development | 3 | 1 | 0.0098302 | 1 |
| GO:0003138 | BP | primary heart field specification | 3 | 1 | 0.0099138 | 1 |
| GO:0060157 | BP | urinary bladder development | 4 | 1 | 0.0101397 | 1 |
| GO:0009256 | BP | 10-formyltetrahydrofolate metabolic process | 5 | 1 | 0.0101432 | 1 |
| GO:1902379 | MF | chemoattractant activity involved in axon guidance | 2 | 1 | 0.0101929 | 1 |
| GO:0021953 | BP | central nervous system neuron differentiation | 186 | 3 | 0.0102959 | 1 |
| GO:0001025 | MF | RNA polymerase III general transcription initiation factor binding | 3 | 1 | 0.0103155 | 1 |
| GO:0001156 | MF | TFIIIC-class transcription factor complex binding | 3 | 1 | 0.0103155 | 1 |
| GO:0048818 | BP | positive regulation of hair follicle maturation | 5 | 1 | 0.0103953 | 1 |
| GO:0001002 | MF | RNA polymerase III type 1 promoter sequence-specific DNA binding | 3 | 1 | 0.0103974 | 1 |
| GO:0001003 | MF | RNA polymerase III type 2 promoter sequence-specific DNA binding | 3 | 1 | 0.0103974 | 1 |
| GO:0080084 | MF | 5S rDNA binding | 3 | 1 | 0.0103974 | 1 |
| GO:0003213 | BP | cardiac right atrium morphogenesis | 2 | 1 | 0.0106682 | 1 |
| GO:0048852 | BP | diencephalon morphogenesis | 3 | 1 | 0.0108245 | 1 |
| GO:0106006 | MF | cytoskeletal protein-membrane anchor activity | 3 | 1 | 0.0109384 | 1 |
| GO:0060750 | BP | epithelial cell proliferation involved in mammary gland duct elongation | 3 | 1 | 0.0110411 | 1 |
| GO:0060751 | BP | branch elongation involved in mammary gland duct branching | 3 | 1 | 0.0110411 | 1 |
| GO:0038031 | BP | non-canonical Wnt signaling pathway via JNK cascade | 6 | 1 | 0.0113371 | 1 |
| GO:0098732 | BP | macromolecule deacylation | 101 | 2 | 0.0116357 | 1 |
| GO:0070245 | BP | positive regulation of thymocyte apoptotic process | 5 | 1 | 0.0118200 | 1 |
| GO:0034983 | BP | peptidyl-lysine deacetylation | 7 | 1 | 0.0118657 | 1 |
| GO:0001938 | BP | positive regulation of endothelial cell proliferation | 107 | 2 | 0.0118838 | 1 |
| GO:0033138 | BP | positive regulation of peptidyl-serine phosphorylation | 91 | 2 | 0.0120043 | 1 |
| GO:0100012 | BP | regulation of heart induction by canonical Wnt signaling pathway | 5 | 1 | 0.0121810 | 1 |
| GO:0060029 | BP | convergent extension involved in organogenesis | 6 | 1 | 0.0122571 | 1 |
| GO:0061702 | CC | inflammasome complex | 15 | 1 | 0.0127027 | 1 |
| GO:0036515 | BP | serotonergic neuron axon guidance | 4 | 1 | 0.0128115 | 1 |
| GO:0097476 | BP | spinal cord motor neuron migration | 4 | 1 | 0.0129507 | 1 |
| GO:0015386 | MF | potassium:proton antiporter activity | 9 | 1 | 0.0131411 | 1 |
| GO:0045927 | BP | positive regulation of growth | 250 | 3 | 0.0132418 | 1 |
| GO:0036514 | BP | dopaminergic neuron axon guidance | 5 | 1 | 0.0134260 | 1 |
| GO:1904938 | BP | planar cell polarity pathway involved in axon guidance | 5 | 1 | 0.0134260 | 1 |
| GO:0018105 | BP | peptidyl-serine phosphorylation | 282 | 3 | 0.0134792 | 1 |
| GO:0015385 | MF | sodium:proton antiporter activity | 10 | 1 | 0.0135356 | 1 |
| GO:1901216 | BP | positive regulation of neuron death | 91 | 2 | 0.0139154 | 1 |
| GO:0071374 | BP | cellular response to parathyroid hormone stimulus | 8 | 1 | 0.0139668 | 1 |
| GO:0071233 | BP | cellular response to leucine | 10 | 1 | 0.0141602 | 1 |
| GO:0060340 | BP | positive regulation of type I interferon-mediated signaling pathway | 13 | 1 | 0.0142616 | 1 |
| GO:0038030 | BP | non-canonical Wnt signaling pathway via MAPK cascade | 7 | 1 | 0.0143467 | 1 |
| GO:0003307 | BP | regulation of Wnt signaling pathway involved in heart development | 9 | 1 | 0.0144283 | 1 |
| GO:0060090 | MF | molecular adaptor activity | 302 | 3 | 0.0144754 | 1 |
| GO:0002862 | BP | negative regulation of inflammatory response to antigenic stimulus | 14 | 1 | 0.0148018 | 1 |
| GO:0044851 | BP | hair cycle phase | 9 | 1 | 0.0149027 | 1 |
| GO:0048819 | BP | regulation of hair follicle maturation | 9 | 1 | 0.0149027 | 1 |
| GO:0005451 | MF | monovalent cation:proton antiporter activity | 11 | 1 | 0.0152620 | 1 |
| GO:0021954 | BP | central nervous system neuron development | 78 | 2 | 0.0153361 | 1 |
| GO:0071107 | BP | response to parathyroid hormone | 10 | 1 | 0.0155003 | 1 |
# results adjusted for age, sex, smoking
fact850_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_850k_092520.txt', sep = "\t", header = T)
fact450_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_450k_092520.txt', sep = "\t", header = T)
chilePBMC_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_PBMCs_DVPs_updated-results_2020-11-29/age-sex-smoking.txt', sep = "\t", header = T)
chileBuccal_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_buccal_DVPs_updated-results_2020-11-29/age-sex-smoking.txt', sep = "\t", header = T)
fact850_DVP = fact850_DVP[fact850_DVP$cpg %in% allCpg,]
fact450_DVP = fact450_DVP[fact450_DVP$cpg %in% allCpg,]
chilePBMC_DVP = chilePBMC_DVP[chilePBMC_DVP$cpg %in% allCpg,]
chileBuccal_DVP = chileBuccal_DVP[chileBuccal_DVP$cpg %in% allCpg,]
write.table(fact850_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_850k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(fact450_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_450k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chilePBMC_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_DVP_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chileBuccal_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-age-sex-smoking_DVP_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
# results adjusted for age, sex, smoking, cells
fact850cell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_850k_092520.txt', sep = "\t", header = T)
fact450cell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_450k_092520.txt', sep = "\t", header = T)
chilePBMCcell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_PBMCs_DVPs_updated-results_2020-11-29/cell-age-sex-smoking.txt', sep = "\t", header = T)
chileBuccalcell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_buccal_DVPs_updated-results_2020-11-29/cell-age-sex-smoking.txt', sep = "\t", header = T)
fact850cell_DVP = fact850cell_DVP[fact850cell_DVP$cpg %in% allCpg,]
fact450cell_DVP = fact450cell_DVP[fact450cell_DVP$cpg %in% allCpg,]
chilePBMCcell_DVP = chilePBMCcell_DVP[chilePBMCcell_DVP$cpg %in% allCpg,]
chileBuccalcell_DVP = chileBuccalcell_DVP[chileBuccalcell_DVP$cpg %in% allCpg,]
write.table(fact850cell_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_850k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(fact450cell_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_450k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chilePBMCcell_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_DVP_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chileBuccalcell_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-cell-age-sex-smoking_DVP_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
cd /Users/annebozack/Documents/arsenic_meta/generic-metal
MARKER "cpg"
EFFECT "DiffLevene"
PVAL "P.Value"
STDERR "std_err"
SCHEME STDERR
# SCHEME STDERR command and weights effect size estimates using the inverse of the corresponding standard errors
# no cell type adjustment, blood only
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_DVP_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/blood_no_cell_common_DVP_120420 .tbl
ANALYZE
# no cell type adjustment, all samples
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_DVP_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-age-sex-smoking_DVP_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/all_no_cell_common_DVP_120420 .tbl
ANALYZE
# cell type adjustment, blood only
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_DVP_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/blood_cell_common_DVP_120420 .tbl
ANALYZE
# cell type adjustment, all samples
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_DVP_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-cell-age-sex-smoking_DVP_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/all_cell_common_DVP_120420 .tbl
ANALYZE
metal_blood_noCell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/blood_no_cell_common_DVP_1204201.tbl', sep = "\t")
metal_blood_noCell_DVP = metalProcess(metal_blood_noCell_DVP)
write.csv(metal_blood_noCell_DVP, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DVP_blood_no_cell_common_120420.csv')
# Significant probes
# Nominal P-value
table(metal_blood_noCell_DVP$P.value < 0.05)
# FALSE TRUE
# 350920 26431
# FDR
table(metal_blood_noCell_DVP$P.FDR < 0.05)
# FALSE TRUE
# 377326 25
table(metal_blood_noCell_DVP$P.FDR < 0.1)
# FALSE TRUE
# 377306 45
# Bonferroni
table(metal_blood_noCell_DVP$P.Bonf < 0.05)
# FALSE TRUE
# 377346 5
# GO analysis, FDR < 0.1 probes
go_metal_blood_noCell_DVP = gometh(sig.cpg = metal_blood_noCell_DVP$Name[metal_blood_noCell_DVP$P.FDR < 0.1], all.cpg = metal_blood_noCell_DVP$Name, array.type = '450K', anno = annAll2)
go_metal_blood_noCell_DVP = go_metal_blood_noCell_DVP[order(go_metal_blood_noCell_DVP$P.DE),]
table(go_metal_blood_noCell_DVP$P.DE<0.05)
# FALSE TRUE
# 22453 130
table(go_metal_blood_noCell_DVP$FDR<0.05)
# FALSE
# 22583
write.csv(go_metal_blood_noCell_DVP[go_metal_blood_noCell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DVP_blood_noCell_common_120420.csv')
# KEGG analysis, FDR < 0.1 probes
kegg_metal_blood_noCell_DVP = gometh(sig.cpg = metal_blood_noCell_DVP$Name[metal_blood_noCell_DVP$P.FDR < 0.1], all.cpg = metal_blood_noCell_DVP$Name, array.type = '450K', collection = 'KEGG', anno = annAll2)
kegg_metal_blood_noCell_DVP = kegg_metal_blood_noCell_DVP[order(kegg_metal_blood_noCell_DVP$P.DE),]
table(kegg_metal_blood_noCell_DVP$P.DE<0.05)
# FALSE TRUE
# 335 5
table(kegg_metal_blood_noCell_DVP$FDR<0.05)
# FALSE
# 340
write.csv(kegg_metal_blood_noCell_DVP[kegg_metal_blood_noCell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DVP_blood_noCell_common_120420.csv')
# Plotting
gg_qqplot(metal_blood_noCell_DVP$P.value)
quartz.save('qq_metal_blood_noCell_DVP_120420.png', type = "png", dpi = 300)
manhattan_meta(metal_blood_noCell_DVP, FDR=T)
quartz.save('manhattan_metal_blood_noCell_DVP_120420.png', type = "png", dpi = 300)
volcano_meta(metal_blood_noCell_DVP, FDR = TRUE)
quartz.save('volcano_metal_blood_noCell_DVP_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_blood_noCell_DVP_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_blood_noCell_DVP_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_blood_noCell_DVP_120420.png")
| X | Name | Effect | StdErr | P.value | Direction | P.FDR | P.Bonf | chr | pos | UCSC_RefGene_Name | UCSC_RefGene_Group |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 321132 | cg23281729 | 0.9488 | 0.1212 | 0.00e+00 | -++ | 0.0000000 | 0.0000000 | chr18 | 78005477 | PARD6G | TSS200 |
| 268961 | cg18971529 | 0.3420 | 0.0614 | 0.00e+00 | ++- | 0.0037974 | 0.0094036 | chr21 | 30391563 | RWDD2B | 1stExon |
| 50934 | cg03205258 | 0.5963 | 0.1076 | 0.00e+00 | +++ | 0.0037974 | 0.0113922 | chr22 | 19929274 | TXNRD2;COMT;COMT | 1stExon;1stExon;5’UTR |
| 10618 | cg00629117 | 0.9092 | 0.1674 | 1.00e-07 | +++ | 0.0052395 | 0.0209581 | chr16 | 1844932 | IGFALS;IGFALS;IGFALS | TSS200;TSS1500;TSS1500 |
| 309909 | cg22387890 | 0.5327 | 0.0993 | 1.00e-07 | +++ | 0.0060852 | 0.0304258 | chr7 | 6145595 | USP42 | 5’UTR |
| 163279 | cg11032634 | 0.6573 | 0.1251 | 1.00e-07 | +++ | 0.0092765 | 0.0556593 | chr22 | 19929254 | TXNRD2;COMT | 1stExon;TSS200 |
| 189046 | cg13054212 | 0.1060 | 0.0204 | 2.00e-07 | +++ | 0.0095797 | 0.0791305 | chr4 | 186356202 | C4orf47 | Body |
| 282819 | cg20074307 | 0.0884 | 0.0171 | 2.00e-07 | +++ | 0.0095797 | 0.0892812 | chr14 | 55092491 | SAMD4A;SAMD4A | Body;Body |
| 261543 | cg18380742 | 0.1049 | 0.0203 | 2.00e-07 | +++ | 0.0095797 | 0.0915831 | chr1 | 61674366 | NFIA;NFIA;NFIA;NFIA | Body;Body;Body;Body |
| 32578 | cg02026246 | 0.1680 | 0.0328 | 3.00e-07 | +++ | 0.0095797 | 0.1129412 | chr11 | 22687589 | GAS2 | TSS1500 |
| 374163 | cg27425262 | 0.7281 | 0.1422 | 3.00e-07 | +++ | 0.0095797 | 0.1152807 | chr2 | 113953981 | PSD4;LOC440839 | Body;Body |
| 145256 | cg09692492 | -0.3016 | 0.0590 | 3.00e-07 | — | 0.0095797 | 0.1192052 | chr22 | 23744717 | ZDHHC8P | Body |
| 199880 | cg13797228 | 0.1148 | 0.0225 | 3.00e-07 | +++ | 0.0095797 | 0.1270541 | chr3 | 126076243 | KLF15 | TSS200 |
| 237588 | cg16511076 | 0.1132 | 0.0223 | 4.00e-07 | +++ | 0.0095797 | 0.1435821 | chr4 | 48887480 | OCIAD2;OCIAD2 | 3’UTR;3’UTR |
| 171628 | cg11691429 | 0.1834 | 0.0361 | 4.00e-07 | +++ | 0.0095797 | 0.1436953 | chr2 | 947634 | SNTG2 | Body |
| 149284 | cg09996597 | 0.4748 | 0.0945 | 5.00e-07 | +++ | 0.0118134 | 0.1890151 | chr16 | 1844927 | IGFALS;IGFALS;IGFALS | TSS200;TSS1500;TSS1500 |
| 2783 | cg00156336 | -0.1921 | 0.0384 | 5.00e-07 | — | 0.0121840 | 0.2071280 | chr2 | 75788423 | FAM176A;FAM176A | 5’UTR;TSS1500 |
| 124685 | cg08207566 | 0.1099 | 0.0224 | 1.00e-06 | +++ | 0.0205510 | 0.3699172 | chr4 | 174086461 | ||
| 93087 | cg06039392 | 0.1376 | 0.0282 | 1.00e-06 | +++ | 0.0205954 | 0.3913130 | chr4 | 187476953 | MTNR1A | TSS1500 |
| 41466 | cg02593924 | 0.2792 | 0.0583 | 1.70e-06 | +++ | 0.0318107 | 0.6362138 | chr16 | 1844998 | IGFALS;IGFALS;IGFALS | TSS200;TSS1500;TSS1500 |
| 313664 | cg22712983 | -0.2209 | 0.0464 | 1.90e-06 | –+ | 0.0332583 | 0.7139481 | chr2 | 219187374 | PNKD;PNKD | TSS1500;Body |
| 325001 | cg23602489 | 0.1012 | 0.0213 | 1.90e-06 | +++ | 0.0332583 | 0.7316836 | chr7 | 101508949 | CUX1;CUX1;CUX1 | Body;Body;Body |
| 121859 | cg08015590 | -0.4238 | 0.0896 | 2.30e-06 | — | 0.0372265 | 0.8562094 | chr7 | 2281924 | NUDT1;NUDT1;NUDT1;NUDT1;NUDT1;NUDT1;FTSJ2;NUDT1;NUDT1;NUDT1 | 5’UTR;5’UTR;1stExon;TSS1500;5’UTR;5’UTR;TSS200;1stExon;5’UTR;TSS1500 |
| 135062 | cg08942080 | 0.1515 | 0.0321 | 2.40e-06 | +++ | 0.0383483 | 0.9203591 | chr12 | 124821568 | NCOR2;NCOR2 | Body;Body |
| 169144 | cg11494866 | 0.1017 | 0.0218 | 3.10e-06 | +++ | 0.0463085 | 1.0000000 | chr8 | 42695070 | THAP1;THAP1 | Body;Body |
| 516 | cg00026731 | -0.1223 | 0.0264 | 3.60e-06 | — | 0.0521470 | 1.0000000 | chr18 | 55254092 | FECH;FECH | TSS200;TSS200 |
| 190991 | cg13221086 | 0.1023 | 0.0223 | 4.30e-06 | +++ | 0.0595935 | 1.0000000 | chr3 | 31809318 | OSBPL10 | Body |
| 293675 | cg21004290 | 0.1140 | 0.0249 | 4.50e-06 | +++ | 0.0611578 | 1.0000000 | chr8 | 131250320 | ASAP1 | Body |
| 301219 | cg21623748 | 0.0943 | 0.0206 | 4.80e-06 | +++ | 0.0625101 | 1.0000000 | chr12 | 54378787 | HOXC10 | TSS200 |
| 9019 | cg00534624 | 0.2751 | 0.0604 | 5.20e-06 | +++ | 0.0632577 | 1.0000000 | chr16 | 1845096 | IGFALS;IGFALS;IGFALS | TSS200;TSS1500;TSS1500 |
| 194801 | cg13483984 | 0.1164 | 0.0256 | 5.50e-06 | +++ | 0.0632577 | 1.0000000 | chr1 | 224580455 | WDR26;WDR26 | Body;Body |
| 268251 | cg18907098 | 0.0733 | 0.0161 | 5.50e-06 | +++ | 0.0632577 | 1.0000000 | chr4 | 512994 | PIGG;PIGG | Body;Body |
| 168599 | cg11440940 | 0.0987 | 0.0217 | 5.50e-06 | +++ | 0.0632577 | 1.0000000 | chr19 | 8510764 | HNRNPM;HNRNPM | Body;Body |
| 259345 | cg18206914 | 0.0839 | 0.0185 | 5.80e-06 | +++ | 0.0640024 | 1.0000000 | chr22 | 50963825 | SCO2;SCO2;SCO2;SCO2 | 5’UTR;5’UTR;5’UTR;5’UTR |
| 156274 | cg10502904 | 0.1611 | 0.0356 | 6.10e-06 | +++ | 0.0640024 | 1.0000000 | chr10 | 131565289 | MGMT | 3’UTR |
| 132616 | cg08770961 | 0.2938 | 0.0651 | 6.30e-06 | +++ | 0.0640024 | 1.0000000 | chr16 | 66956122 | RRAD;RRAD | Body;Body |
| 59640 | cg03770962 | 0.1059 | 0.0235 | 6.40e-06 | +++ | 0.0640024 | 1.0000000 | chr7 | 148477754 | CUL1 | Body |
| 64658 | cg04111999 | 0.0991 | 0.0220 | 6.50e-06 | +++ | 0.0640024 | 1.0000000 | chr10 | 22615540 | BMI1 | Body |
| 335850 | cg24454243 | -0.2036 | 0.0452 | 6.70e-06 | — | 0.0640024 | 1.0000000 | chr7 | 105221985 | EFCAB10 | TSS200 |
| 229928 | cg15931233 | 0.0956 | 0.0212 | 6.80e-06 | +++ | 0.0640024 | 1.0000000 | chr5 | 53455496 | ARL15 | Body |
| 80568 | cg05169951 | 0.1850 | 0.0411 | 7.00e-06 | +++ | 0.0640024 | 1.0000000 | chr16 | 3017955 | KREMEN2;PAQR4;KREMEN2 | Body;TSS1500;Body |
| 178342 | cg12175949 | 0.3443 | 0.0769 | 7.60e-06 | +++ | 0.0679591 | 1.0000000 | chr22 | 19929286 | TXNRD2;COMT;COMT | 1stExon;1stExon;5’UTR |
| 259615 | cg18228116 | 0.3258 | 0.0735 | 9.30e-06 | -++ | 0.0820168 | 1.0000000 | chr10 | 133995345 | JAKMIP3 | 3’UTR |
| 349119 | cg25499746 | 0.0792 | 0.0179 | 9.90e-06 | +++ | 0.0845695 | 1.0000000 | chr6 | 16346054 | ATXN1;ATXN1 | 5’UTR;5’UTR |
| 48009 | cg03004999 | -0.0816 | 0.0186 | 1.15e-05 | — | 0.0960149 | 1.0000000 | chr7 | 43152125 | HECW1 | TSS200 |
| 26185 | cg01614020 | 0.2522 | 0.0577 | 1.24e-05 | +++ | 0.1014746 | 1.0000000 | chr8 | 24814137 | NEFL | TSS200 |
| 240531 | cg16707423 | 0.0797 | 0.0183 | 1.29e-05 | +++ | 0.1016671 | 1.0000000 | chr1 | 227167020 | CABC1 | Body |
| 38724 | cg02415779 | 0.1130 | 0.0259 | 1.32e-05 | -++ | 0.1016671 | 1.0000000 | chr22 | 18527778 | ||
| 323330 | cg23463533 | 0.0930 | 0.0214 | 1.33e-05 | +++ | 0.1016671 | 1.0000000 | chr7 | 154473289 | DPP6;DPP6;DPP6 | Body;Body;Body |
| 129911 | cg08575722 | -0.1195 | 0.0275 | 1.36e-05 | — | 0.1016671 | 1.0000000 | chr11 | 32421845 | WT1;WT1;WT1;WT1 | Body;Body;Body;Body |
| 70352 | cg04485956 | 0.2005 | 0.0461 | 1.38e-05 | +++ | 0.1016671 | 1.0000000 | chr2 | 1859071 | MYT1L | Body |
| 80361 | cg05157266 | 0.1358 | 0.0313 | 1.40e-05 | +++ | 0.1016671 | 1.0000000 | chr2 | 183901614 | NCKAP1;NCKAP1 | Body;Body |
| 320947 | cg23268677 | 0.2705 | 0.0625 | 1.50e-05 | +++ | 0.1051691 | 1.0000000 | chr22 | 19929097 | TXNRD2;COMT | Body;TSS200 |
| 353609 | cg25880954 | 0.7380 | 0.1705 | 1.50e-05 | +++ | 0.1051691 | 1.0000000 | chr1 | 47900630 | MGC12982;FOXD2 | TSS1500;TSS1500 |
| 297153 | cg21270743 | 0.0928 | 0.0215 | 1.61e-05 | +++ | 0.1061227 | 1.0000000 | chr1 | 156475001 | ||
| 191701 | cg13279009 | 0.0804 | 0.0187 | 1.63e-05 | -++ | 0.1061227 | 1.0000000 | chr2 | 24584023 | ITSN2;ITSN2;ITSN2 | TSS1500;TSS1500;TSS1500 |
| 305009 | cg21951425 | -0.1330 | 0.0309 | 1.63e-05 | — | 0.1061227 | 1.0000000 | chr15 | 26108612 | ATP10A | TSS1500 |
| 291461 | cg20805880 | 0.1028 | 0.0239 | 1.68e-05 | +++ | 0.1061227 | 1.0000000 | chr15 | 73367293 | NEO1 | Body |
| 332989 | cg24215973 | 0.2223 | 0.0517 | 1.73e-05 | +++ | 0.1061227 | 1.0000000 | chr2 | 240111563 | HDAC4 | Body |
| 282764 | cg20070659 | 0.2554 | 0.0595 | 1.76e-05 | -++ | 0.1061227 | 1.0000000 | chr4 | 188736336 | ||
| 25526 | cg01570086 | -0.1220 | 0.0284 | 1.77e-05 | — | 0.1061227 | 1.0000000 | chr15 | 74833080 | ARID3B | TSS1500 |
| 176205 | cg12024822 | 0.1823 | 0.0425 | 1.81e-05 | +++ | 0.1061227 | 1.0000000 | chr6 | 90597394 | ||
| 193732 | cg13423098 | 0.1394 | 0.0325 | 1.81e-05 | +++ | 0.1061227 | 1.0000000 | chr15 | 23807234 | ||
| 11224 | cg00668103 | 0.1128 | 0.0263 | 1.82e-05 | +++ | 0.1061227 | 1.0000000 | chr7 | 100084730 | C7orf51 | Body |
| 196530 | cg13587236 | 0.0904 | 0.0211 | 1.83e-05 | +++ | 0.1061227 | 1.0000000 | chr9 | 128472496 | ||
| 361112 | cg26453295 | 0.0812 | 0.0190 | 1.94e-05 | +++ | 0.1093224 | 1.0000000 | chr19 | 54851740 | LILRA4 | TSS1500 |
| 329980 | cg23990236 | 0.1245 | 0.0292 | 1.96e-05 | -++ | 0.1093224 | 1.0000000 | chr1 | 12220146 | ||
| 223604 | cg15439717 | 0.1095 | 0.0257 | 1.98e-05 | +++ | 0.1093224 | 1.0000000 | chr13 | 23993016 | SACS | 5’UTR |
| 309271 | cg22336633 | -0.1142 | 0.0268 | 2.00e-05 | — | 0.1093224 | 1.0000000 | chr11 | 17099688 | RPS13 | TSS1500 |
| 127440 | cg08400962 | 0.1029 | 0.0242 | 2.04e-05 | +++ | 0.1094849 | 1.0000000 | chr19 | 34112316 | CHST8;CHST8 | TSS1500;TSS1500 |
| 299250 | cg21476203 | 0.1083 | 0.0254 | 2.06e-05 | +++ | 0.1094849 | 1.0000000 | chr8 | 144874281 | SCRIB;SCRIB | Body;Body |
| 39898 | cg02492873 | 0.1056 | 0.0248 | 2.14e-05 | ++- | 0.1111146 | 1.0000000 | chr2 | 25193821 | DNAJC27 | Body |
| 110491 | cg07219314 | -0.1568 | 0.0369 | 2.17e-05 | — | 0.1111146 | 1.0000000 | chr22 | 23744725 | ZDHHC8P | Body |
| 153889 | cg10322744 | 0.4290 | 0.1011 | 2.18e-05 | +++ | 0.1111146 | 1.0000000 | chr12 | 98910138 | TMPO;TMPO;TMPO;LOC100128191 | Body;Body;Body;TSS200 |
| 203197 | cg14002714 | 0.1309 | 0.0310 | 2.37e-05 | -++ | 0.1192429 | 1.0000000 | chr14 | 56095810 | KTN1;KTN1;KTN1;KTN1 | Body;Body;Body;Body |
| 110227 | cg07202461 | 0.0845 | 0.0201 | 2.53e-05 | +++ | 0.1257671 | 1.0000000 | chr18 | 19406765 | MIB1;MIR133A1 | Body;TSS1500 |
| 50532 | cg03176729 | 0.3304 | 0.0785 | 2.59e-05 | +++ | 0.1269762 | 1.0000000 | chr10 | 124222607 | HTRA1 | Body |
| 193559 | cg13411311 | -0.0913 | 0.0217 | 2.66e-05 | — | 0.1277739 | 1.0000000 | chr2 | 241095989 | ||
| 157333 | cg10577216 | -0.1585 | 0.0377 | 2.68e-05 | — | 0.1277739 | 1.0000000 | chr6 | 143265045 | HIVEP2 | 5’UTR |
| 111485 | cg07290190 | 0.0927 | 0.0221 | 2.85e-05 | ++- | 0.1313439 | 1.0000000 | chr4 | 121992756 | C4orf31 | 5’UTR |
| 59636 | cg03770787 | -0.2358 | 0.0564 | 2.87e-05 | — | 0.1313439 | 1.0000000 | chr15 | 65652019 | IGDCC3 | Body |
| 96749 | cg06319359 | 0.0756 | 0.0181 | 2.88e-05 | +++ | 0.1313439 | 1.0000000 | chr1 | 22109595 | USP48;USP48;USP48;USP48 | 5’UTR;5’UTR;1stExon;1stExon |
| 364539 | cg26706070 | 0.0913 | 0.0218 | 2.89e-05 | +++ | 0.1313439 | 1.0000000 | chr16 | 31119936 | BCKDK;BCKDK | 5’UTR;5’UTR |
| 185794 | cg12778178 | 0.1033 | 0.0247 | 2.93e-05 | +++ | 0.1313439 | 1.0000000 | chr20 | 62583555 | UCKL1AS;UCKL1 | TSS1500;Body |
| 147224 | cg09845489 | 0.2355 | 0.0564 | 3.00e-05 | +++ | 0.1313439 | 1.0000000 | chr7 | 157667853 | PTPRN2;PTPRN2;PTPRN2 | Body;Body;Body |
| 259108 | cg18190030 | -0.1190 | 0.0285 | 3.03e-05 | +– | 0.1313439 | 1.0000000 | chr1 | 234348636 | SLC35F3 | Body |
| 58766 | cg03717570 | 0.1286 | 0.0308 | 3.04e-05 | +++ | 0.1313439 | 1.0000000 | chr17 | 73316496 | GRB2;GRB2 | Body;Body |
| 155786 | cg10468535 | 0.1263 | 0.0303 | 3.06e-05 | +++ | 0.1313439 | 1.0000000 | chr7 | 157792053 | PTPRN2;PTPRN2;PTPRN2 | Body;Body;Body |
| 125889 | cg08285768 | 0.0863 | 0.0208 | 3.29e-05 | +++ | 0.1354434 | 1.0000000 | chr15 | 86038622 | AKAP13;AKAP13 | Body;Body |
| 116632 | cg07642445 | 0.0668 | 0.0161 | 3.30e-05 | +++ | 0.1354434 | 1.0000000 | chr6 | 27855795 | ||
| 261990 | cg18414754 | 0.1826 | 0.0440 | 3.32e-05 | +++ | 0.1354434 | 1.0000000 | chr3 | 138668832 | C3orf72 | Body |
| 235393 | cg16353272 | 0.0827 | 0.0199 | 3.34e-05 | +++ | 0.1354434 | 1.0000000 | chr16 | 2124240 | TSC2;TSC2;TSC2 | Body;Body;Body |
| 295936 | cg21185289 | 0.2892 | 0.0698 | 3.38e-05 | +++ | 0.1354434 | 1.0000000 | chr2 | 74743437 | TLX2 | 3’UTR |
| 351214 | cg25674826 | 0.2435 | 0.0587 | 3.38e-05 | +++ | 0.1354434 | 1.0000000 | chr21 | 35446543 | MRPS6;SLC5A3 | Body;5’UTR |
| 253963 | cg17805202 | 0.1087 | 0.0262 | 3.45e-05 | +++ | 0.1354434 | 1.0000000 | chr1 | 239937440 | CHRM3 | 5’UTR |
| 90239 | cg05850971 | 0.0924 | 0.0223 | 3.53e-05 | +++ | 0.1354434 | 1.0000000 | chr6 | 32135027 | EGFL8 | Body |
| 12204 | cg00729699 | -0.0914 | 0.0221 | 3.58e-05 | — | 0.1354434 | 1.0000000 | chr8 | 21918075 | EPB49;EPB49;EPB49;EPB49;EPB49;EPB49 | 5’UTR;5’UTR;5’UTR;5’UTR;5’UTR;5’UTR |
| 363304 | cg26618618 | 0.0956 | 0.0231 | 3.58e-05 | +++ | 0.1354434 | 1.0000000 | chr11 | 95661178 | ||
| 355638 | cg26051433 | 0.0958 | 0.0232 | 3.61e-05 | +++ | 0.1354434 | 1.0000000 | chr10 | 75001410 | FAM149B1 | 3’UTR |
| 11047 | cg00657529 | 0.0832 | 0.0201 | 3.61e-05 | +++ | 0.1354434 | 1.0000000 | chr6 | 31698687 | CLIC1;DDAH2 | Body;TSS1500 |
| X | ONTOLOGY | TERM | N | DE | P.DE | FDR |
|---|---|---|---|---|---|---|
| GO:0004325 | MF | ferrochelatase activity | 1 | 1 | 0.0015112 | 1 |
| GO:0042053 | BP | regulation of dopamine metabolic process | 17 | 2 | 0.0018929 | 1 |
| GO:0042069 | BP | regulation of catecholamine metabolic process | 17 | 2 | 0.0018929 | 1 |
| GO:0015036 | MF | disulfide oxidoreductase activity | 39 | 2 | 0.0027763 | 1 |
| GO:0070541 | BP | response to platinum ion | 3 | 1 | 0.0039000 | 1 |
| GO:0016363 | CC | nuclear matrix | 103 | 3 | 0.0039500 | 1 |
| GO:2000815 | BP | regulation of mRNA stability involved in response to oxidative stress | 2 | 1 | 0.0041977 | 1 |
| GO:0031337 | BP | positive regulation of sulfur amino acid metabolic process | 1 | 1 | 0.0061113 | 1 |
| GO:0050668 | BP | positive regulation of homocysteine metabolic process | 1 | 1 | 0.0061113 | 1 |
| GO:0042417 | BP | dopamine metabolic process | 33 | 2 | 0.0061305 | 1 |
| GO:0016667 | MF | oxidoreductase activity, acting on a sulfur group of donors | 57 | 2 | 0.0063848 | 1 |
| GO:0034399 | CC | nuclear periphery | 124 | 3 | 0.0065066 | 1 |
| GO:0051267 | MF | CP2 mannose-ethanolamine phosphotransferase activity | 1 | 1 | 0.0065613 | 1 |
| GO:0003908 | MF | methylated-DNA-[protein]-cysteine S-methyltransferase activity | 1 | 1 | 0.0074068 | 1 |
| GO:0050666 | BP | regulation of homocysteine metabolic process | 2 | 1 | 0.0075457 | 1 |
| GO:0001544 | BP | initiation of primordial ovarian follicle growth | 2 | 1 | 0.0083648 | 1 |
| GO:0000301 | BP | retrograde transport, vesicle recycling within Golgi | 2 | 1 | 0.0085027 | 1 |
| GO:0004416 | MF | hydroxyacylglutathione hydrolase activity | 2 | 1 | 0.0087442 | 1 |
| GO:0019243 | BP | methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione | 2 | 1 | 0.0087442 | 1 |
| GO:0051377 | MF | mannose-ethanolamine phosphotransferase activity | 4 | 1 | 0.0090417 | 1 |
| GO:0008502 | MF | melatonin receptor activity | 3 | 1 | 0.0090824 | 1 |
| GO:0045764 | BP | positive regulation of cellular amino acid metabolic process | 3 | 1 | 0.0091048 | 1 |
| GO:0016206 | MF | catechol O-methyltransferase activity | 2 | 1 | 0.0092874 | 1 |
| GO:0102084 | MF | L-dopa O-methyltransferase activity | 2 | 1 | 0.0092874 | 1 |
| GO:0102938 | MF | orcinol O-methyltransferase activity | 2 | 1 | 0.0092874 | 1 |
| GO:0006584 | BP | catecholamine metabolic process | 46 | 2 | 0.0094643 | 1 |
| GO:0009712 | BP | catechol-containing compound metabolic process | 46 | 2 | 0.0094643 | 1 |
| GO:0016036 | BP | cellular response to phosphate starvation | 2 | 1 | 0.0096037 | 1 |
| GO:0031335 | BP | regulation of sulfur amino acid metabolic process | 3 | 1 | 0.0096910 | 1 |
| GO:0051596 | BP | methylglyoxal catabolic process | 3 | 1 | 0.0106621 | 1 |
| GO:0061727 | BP | methylglyoxal catabolic process to lactate | 3 | 1 | 0.0106621 | 1 |
| GO:0005759 | CC | mitochondrial matrix | 452 | 4 | 0.0107974 | 1 |
| GO:0010610 | BP | regulation of mRNA stability involved in response to stress | 3 | 1 | 0.0109776 | 1 |
| GO:0035814 | BP | negative regulation of renal sodium excretion | 3 | 1 | 0.0110177 | 1 |
| GO:0001786 | MF | phosphatidylserine binding | 56 | 2 | 0.0116723 | 1 |
| GO:1901842 | BP | negative regulation of high voltage-gated calcium channel activity | 4 | 1 | 0.0119888 | 1 |
| GO:0042382 | CC | paraspeckles | 6 | 1 | 0.0126671 | 1 |
| GO:0051176 | BP | positive regulation of sulfur metabolic process | 3 | 1 | 0.0130321 | 1 |
| GO:0042698 | BP | ovulation cycle | 69 | 2 | 0.0133490 | 1 |
| GO:0009438 | BP | methylglyoxal metabolic process | 5 | 1 | 0.0142031 | 1 |
| GO:0008172 | MF | S-methyltransferase activity | 6 | 1 | 0.0142529 | 1 |
| GO:0006513 | BP | protein monoubiquitination | 66 | 2 | 0.0142928 | 1 |
| GO:0045914 | BP | negative regulation of catecholamine metabolic process | 3 | 1 | 0.0143262 | 1 |
| GO:0045963 | BP | negative regulation of dopamine metabolic process | 3 | 1 | 0.0143262 | 1 |
| GO:0016013 | CC | syntrophin complex | 3 | 1 | 0.0147056 | 1 |
| GO:0033238 | BP | regulation of cellular amine metabolic process | 78 | 2 | 0.0147491 | 1 |
| GO:0046501 | BP | protoporphyrinogen IX metabolic process | 10 | 1 | 0.0156773 | 1 |
| GO:0042420 | BP | dopamine catabolic process | 5 | 1 | 0.0160319 | 1 |
| GO:1903527 | BP | positive regulation of membrane tubulation | 4 | 1 | 0.0162069 | 1 |
| GO:1990452 | CC | Parkin-FBXW7-Cul1 ubiquitin ligase complex | 3 | 1 | 0.0162837 | 1 |
| GO:0050773 | BP | regulation of dendrite development | 141 | 3 | 0.0170721 | 1 |
| GO:0042180 | BP | cellular ketone metabolic process | 251 | 3 | 0.0178267 | 1 |
| GO:0032413 | BP | negative regulation of ion transmembrane transporter activity | 72 | 2 | 0.0182638 | 1 |
| GO:0051597 | BP | response to methylmercury | 7 | 1 | 0.0188400 | 1 |
| GO:0071535 | MF | RING-like zinc finger domain binding | 4 | 1 | 0.0190520 | 1 |
| GO:0019614 | BP | catechol-containing compound catabolic process | 6 | 1 | 0.0191770 | 1 |
| GO:0042424 | BP | catecholamine catabolic process | 6 | 1 | 0.0191770 | 1 |
| GO:0042567 | CC | insulin-like growth factor ternary complex | 4 | 1 | 0.0192472 | 1 |
| GO:0042182 | BP | ketone catabolic process | 12 | 1 | 0.0199094 | 1 |
| GO:0016942 | CC | insulin-like growth factor binding protein complex | 5 | 1 | 0.0201819 | 1 |
| GO:0036454 | CC | growth factor complex | 5 | 1 | 0.0201819 | 1 |
| GO:0046916 | BP | cellular transition metal ion homeostasis | 104 | 2 | 0.0202261 | 1 |
| GO:0072341 | MF | modified amino acid binding | 84 | 2 | 0.0204407 | 1 |
| GO:0004791 | MF | thioredoxin-disulfide reductase activity | 7 | 1 | 0.0208452 | 1 |
| GO:0001547 | BP | antral ovarian follicle growth | 8 | 1 | 0.0217342 | 1 |
| GO:1903525 | BP | regulation of membrane tubulation | 6 | 1 | 0.0219949 | 1 |
| GO:0036353 | BP | histone H2A-K119 monoubiquitination | 8 | 1 | 0.0220516 | 1 |
| GO:0034046 | MF | poly(G) binding | 7 | 1 | 0.0226594 | 1 |
| GO:0009008 | MF | DNA-methyltransferase activity | 6 | 1 | 0.0227584 | 1 |
| GO:0006878 | BP | cellular copper ion homeostasis | 12 | 1 | 0.0230298 | 1 |
| GO:0032410 | BP | negative regulation of transporter activity | 83 | 2 | 0.0231043 | 1 |
| GO:0010265 | BP | SCF complex assembly | 6 | 1 | 0.0236882 | 1 |
| GO:0033239 | BP | negative regulation of cellular amine metabolic process | 6 | 1 | 0.0243470 | 1 |
| GO:0042405 | CC | nuclear inclusion body | 12 | 1 | 0.0243529 | 1 |
| GO:0046185 | BP | aldehyde catabolic process | 12 | 1 | 0.0244393 | 1 |
| GO:0016668 | MF | oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor | 11 | 1 | 0.0250461 | 1 |
| GO:0033240 | BP | positive regulation of cellular amine metabolic process | 7 | 1 | 0.0250550 | 1 |
| GO:1904063 | BP | negative regulation of cation transmembrane transport | 86 | 2 | 0.0250751 | 1 |
| GO:0019336 | BP | phenol-containing compound catabolic process | 9 | 1 | 0.0258713 | 1 |
| GO:0000151 | CC | ubiquitin ligase complex | 273 | 3 | 0.0259841 | 1 |
| GO:0055070 | BP | copper ion homeostasis | 14 | 1 | 0.0260912 | 1 |
| GO:0051051 | BP | negative regulation of transport | 456 | 4 | 0.0264663 | 1 |
| GO:0007614 | BP | short-term memory | 10 | 1 | 0.0266638 | 1 |
| GO:0044106 | BP | cellular amine metabolic process | 122 | 2 | 0.0269691 | 1 |
| GO:0006825 | BP | copper ion transport | 15 | 1 | 0.0270306 | 1 |
| GO:0042135 | BP | neurotransmitter catabolic process | 9 | 1 | 0.0279874 | 1 |
| GO:0006307 | BP | DNA dealkylation involved in DNA repair | 10 | 1 | 0.0282932 | 1 |
| GO:0051537 | MF | 2 iron, 2 sulfur cluster binding | 21 | 1 | 0.0287087 | 1 |
| GO:0009308 | BP | amine metabolic process | 131 | 2 | 0.0295977 | 1 |
| GO:0071803 | BP | positive regulation of podosome assembly | 10 | 1 | 0.0296441 | 1 |
| GO:0042762 | BP | regulation of sulfur metabolic process | 13 | 1 | 0.0299326 | 1 |
| GO:0050667 | BP | homocysteine metabolic process | 13 | 1 | 0.0314888 | 1 |
| GO:0071014 | CC | post-mRNA release spliceosomal complex | 13 | 1 | 0.0323889 | 1 |
| GO:0033617 | BP | mitochondrial cytochrome c oxidase assembly | 21 | 1 | 0.0324808 | 1 |
| GO:0048609 | BP | multicellular organismal reproductive process | 769 | 5 | 0.0325911 | 1 |
| GO:0015035 | MF | protein disulfide oxidoreductase activity | 21 | 1 | 0.0331027 | 1 |
| GO:0016254 | BP | preassembly of GPI anchor in ER membrane | 16 | 1 | 0.0331426 | 1 |
| GO:0017085 | BP | response to insecticide | 11 | 1 | 0.0333218 | 1 |
| GO:0046929 | BP | negative regulation of neurotransmitter secretion | 10 | 1 | 0.0333587 | 1 |
| GO:0034766 | BP | negative regulation of ion transmembrane transport | 97 | 2 | 0.0333662 | 1 |
metal_all_noCell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/all_no_cell_common_DVP_1204201.tbl', sep = "\t")
metal_all_noCell_DVP = metalProcess(metal_all_noCell_DVP)
write.csv(metal_all_noCell_DVP, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DVP_all_no_cell_common_120420.csv')
# Significant probes
# Nominal P-value
table(metal_all_noCell_DVP$P.value < 0.05)
# FALSE TRUE
# 352439 24912
# FDR
table(metal_all_noCell_DVP$P.FDR < 0.05)
# FALSE TRUE
# 377331 20
table(metal_all_noCell_DVP$P.FDR < 0.1)
# FALSE TRUE
# 377310 41
# Bonferroni
table(metal_all_noCell_DVP$P.Bonf < 0.05)
# FALSE TRUE
# 377346 5
# GO analysis, FDR < 0.1 probes
go_metal_all_noCell_DVP = gometh(sig.cpg = metal_all_noCell_DVP$Name[metal_all_noCell_DVP$P.FDR < 0.1], all.cpg = metal_all_noCell_DVP$Name, array.type = '450K', anno = annAll2)
go_metal_all_noCell_DVP = go_metal_all_noCell_DVP[order(go_metal_all_noCell_DVP$P.DE),]
table(go_metal_all_noCell_DVP$P.DE<0.05)
# FALSE TRUE
# 22387 196
table(go_metal_all_noCell_DVP$FDR<0.05)
# FALSE
# 22583
write.csv(go_metal_all_noCell_DVP[go_metal_all_noCell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DVP_all_noCell_common_120420.csv')
# KEGG analysis, FDR < 0.1 probes
kegg_metal_all_noCell_DVP = gometh(sig.cpg = metal_all_noCell_DVP$Name[metal_all_noCell_DVP$P.FDR < 0.1], all.cpg = metal_all_noCell_DVP$Name, array.type = '450K', collection = 'KEGG', anno = annAll2)
kegg_metal_all_noCell_DVP = kegg_metal_all_noCell_DVP[order(kegg_metal_all_noCell_DVP$P.DE),]
table(kegg_metal_all_noCell_DVP$P.DE<0.05)
# FALSE TRUE
# 336 4
table(kegg_metal_all_noCell_DVP$FDR<0.05)
# FALSE
# 340
write.csv(kegg_metal_all_noCell_DVP[kegg_metal_all_noCell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DVP_all_noCell_common_120420.csv')
# Plotting
gg_qqplot(metal_all_noCell_DVP$P.value)
quartz.save('qq_metal_all_noCell_DVP_120420.png', type = "png", dpi = 300)
manhattan_meta(metal_all_noCell_DVP, FDR=T)
quartz.save('manhattan_metal_all_noCell_DVP_120420.png', type = "png", dpi = 300)
volcano_meta(metal_all_noCell_DVP, FDR = TRUE)
quartz.save('volcano_metal_all_noCell_DVP_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_all_noCell_DVP_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_all_noCell_DVP_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_all_noCell_DVP_120420.png")
| X | Name | Effect | StdErr | P.value | Direction | P.FDR | P.Bonf | chr | pos | UCSC_RefGene_Name | UCSC_RefGene_Group |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 321132 | cg23281729 | 0.9672 | 0.1110 | 0.00e+00 | -+++ | 0.0000000 | 0.0000000 | chr18 | 78005477 | PARD6G | TSS200 |
| 374163 | cg27425262 | 0.8329 | 0.1216 | 0.00e+00 | ++++ | 0.0000014 | 0.0000029 | chr2 | 113953981 | PSD4;LOC440839 | Body;Body |
| 50934 | cg03205258 | 0.5864 | 0.0973 | 0.00e+00 | ++++ | 0.0002130 | 0.0006389 | chr22 | 19929274 | TXNRD2;COMT;COMT | 1stExon;1stExon;5’UTR |
| 163279 | cg11032634 | 0.6070 | 0.1118 | 1.00e-07 | ++++ | 0.0053971 | 0.0215883 | chr22 | 19929254 | TXNRD2;COMT | 1stExon;TSS200 |
| 189046 | cg13054212 | 0.1029 | 0.0191 | 1.00e-07 | ++++ | 0.0054112 | 0.0270561 | chr4 | 186356202 | C4orf47 | Body |
| 309909 | cg22387890 | 0.4666 | 0.0890 | 2.00e-07 | ++++ | 0.0099055 | 0.0594328 | chr7 | 6145595 | USP42 | 5’UTR |
| 190387 | cg13171197 | 0.1154 | 0.0225 | 3.00e-07 | +-++ | 0.0148622 | 0.1040357 | chr7 | 90916020 | ||
| 268961 | cg18971529 | 0.3009 | 0.0592 | 4.00e-07 | ++– | 0.0150148 | 0.1381105 | chr21 | 30391563 | RWDD2B | 1stExon |
| 76120 | cg04873963 | -0.1042 | 0.0205 | 4.00e-07 | —- | 0.0150148 | 0.1436575 | chr16 | 2518322 | ||
| 516 | cg00026731 | -0.1294 | 0.0255 | 4.00e-07 | —- | 0.0150148 | 0.1501480 | chr18 | 55254092 | FECH;FECH | TSS200;TSS200 |
| 193559 | cg13411311 | -0.0993 | 0.0197 | 4.00e-07 | —- | 0.0151489 | 0.1666382 | chr2 | 241095989 | ||
| 169072 | cg11488033 | 0.3422 | 0.0683 | 5.00e-07 | -+++ | 0.0168487 | 0.2021847 | chr3 | 196705898 | ||
| 2783 | cg00156336 | -0.1763 | 0.0354 | 6.00e-07 | —- | 0.0181854 | 0.2364104 | chr2 | 75788423 | FAM176A;FAM176A | 5’UTR;TSS1500 |
| 145256 | cg09692492 | -0.2570 | 0.0520 | 8.00e-07 | —- | 0.0207220 | 0.2901074 | chr22 | 23744717 | ZDHHC8P | Body |
| 261543 | cg18380742 | 0.0983 | 0.0200 | 9.00e-07 | +++- | 0.0231769 | 0.3476535 | chr1 | 61674366 | NFIA;NFIA;NFIA;NFIA | Body;Body;Body;Body |
| 313664 | cg22712983 | -0.2239 | 0.0460 | 1.10e-06 | –+- | 0.0262259 | 0.4196143 | chr2 | 219187374 | PNKD;PNKD | TSS1500;Body |
| 237588 | cg16511076 | 0.1075 | 0.0222 | 1.30e-06 | +++- | 0.0280572 | 0.4769717 | chr4 | 48887480 | OCIAD2;OCIAD2 | 3’UTR;3’UTR |
| 282819 | cg20074307 | 0.0791 | 0.0165 | 1.60e-06 | +++- | 0.0311503 | 0.5856488 | chr14 | 55092491 | SAMD4A;SAMD4A | Body;Body |
| 353609 | cg25880954 | 0.7123 | 0.1485 | 1.60e-06 | ++++ | 0.0311503 | 0.6120633 | chr1 | 47900630 | MGC12982;FOXD2 | TSS1500;TSS1500 |
| 291461 | cg20805880 | 0.1020 | 0.0213 | 1.70e-06 | ++++ | 0.0311503 | 0.6230065 | chr15 | 73367293 | NEO1 | Body |
| 124685 | cg08207566 | 0.1017 | 0.0218 | 3.00e-06 | +++- | 0.0544284 | 1.0000000 | chr4 | 174086461 | ||
| 178342 | cg12175949 | 0.2930 | 0.0631 | 3.40e-06 | ++++ | 0.0573409 | 1.0000000 | chr22 | 19929286 | TXNRD2;COMT;COMT | 1stExon;1stExon;5’UTR |
| 135062 | cg08942080 | 0.1397 | 0.0301 | 3.50e-06 | ++++ | 0.0573409 | 1.0000000 | chr12 | 124821568 | NCOR2;NCOR2 | Body;Body |
| 219690 | cg15104380 | -0.0789 | 0.0170 | 3.70e-06 | +— | 0.0574026 | 1.0000000 | chr10 | 99285205 | UBTD1 | Body |
| 282709 | cg20066496 | -0.1821 | 0.0394 | 3.80e-06 | —- | 0.0574026 | 1.0000000 | chr15 | 43213993 | TTBK2 | TSS1500 |
| 93087 | cg06039392 | 0.1254 | 0.0272 | 4.10e-06 | +++- | 0.0584615 | 1.0000000 | chr4 | 187476953 | MTNR1A | TSS1500 |
| 309271 | cg22336633 | -0.1142 | 0.0248 | 4.20e-06 | —- | 0.0584615 | 1.0000000 | chr11 | 17099688 | RPS13 | TSS1500 |
| 64658 | cg04111999 | 0.0980 | 0.0214 | 4.60e-06 | ++++ | 0.0616834 | 1.0000000 | chr10 | 22615540 | BMI1 | Body |
| 293675 | cg21004290 | 0.1086 | 0.0238 | 5.00e-06 | ++++ | 0.0651906 | 1.0000000 | chr8 | 131250320 | ASAP1 | Body |
| 346588 | cg25298319 | -0.4235 | 0.0932 | 5.60e-06 | —- | 0.0688970 | 1.0000000 | chr2 | 233217079 | ||
| 32578 | cg02026246 | 0.1322 | 0.0291 | 5.70e-06 | +++- | 0.0688970 | 1.0000000 | chr11 | 22687589 | GAS2 | TSS1500 |
| 339841 | cg24754507 | -0.0947 | 0.0209 | 5.90e-06 | —- | 0.0697038 | 1.0000000 | chr6 | 28481862 | GPX6 | Body |
| 268251 | cg18907098 | 0.0729 | 0.0161 | 6.20e-06 | +++- | 0.0713994 | 1.0000000 | chr4 | 512994 | PIGG;PIGG | Body;Body |
| 171628 | cg11691429 | 0.1555 | 0.0346 | 7.00e-06 | +++- | 0.0781339 | 1.0000000 | chr2 | 947634 | SNTG2 | Body |
| 92754 | cg06013413 | 0.0904 | 0.0202 | 7.40e-06 | -+++ | 0.0795497 | 1.0000000 | chr8 | 627560 | ERICH1 | Body |
| 332456 | cg24168538 | 0.2387 | 0.0534 | 7.80e-06 | ++++ | 0.0795497 | 1.0000000 | chr4 | 35527016 | ||
| 342170 | cg24933709 | 0.1027 | 0.0230 | 7.80e-06 | ++++ | 0.0795497 | 1.0000000 | chr7 | 149120687 | ||
| 23625 | cg01445793 | 0.1780 | 0.0400 | 8.70e-06 | ++++ | 0.0862942 | 1.0000000 | chr17 | 3771578 | CAMKK1;CAMKK1;CAMKK1 | Body;Body;Body |
| 129911 | cg08575722 | -0.1203 | 0.0272 | 1.01e-05 | —- | 0.0965075 | 1.0000000 | chr11 | 32421845 | WT1;WT1;WT1;WT1 | Body;Body;Body;Body |
| 361112 | cg26453295 | 0.0817 | 0.0185 | 1.02e-05 | ++++ | 0.0965075 | 1.0000000 | chr19 | 54851740 | LILRA4 | TSS1500 |
| 305009 | cg21951425 | -0.1306 | 0.0296 | 1.06e-05 | —- | 0.0976511 | 1.0000000 | chr15 | 26108612 | ATP10A | TSS1500 |
| 9817 | cg00581043 | -0.2105 | 0.0480 | 1.15e-05 | —- | 0.1034285 | 1.0000000 | chr6 | 168106129 | ||
| 173107 | cg11797898 | -0.1299 | 0.0297 | 1.19e-05 | —- | 0.1034285 | 1.0000000 | chr7 | 1983375 | MAD1L1;MAD1L1;MAD1L1 | Body;Body;Body |
| 323330 | cg23463533 | 0.0904 | 0.0207 | 1.21e-05 | ++++ | 0.1034285 | 1.0000000 | chr7 | 154473289 | DPP6;DPP6;DPP6 | Body;Body;Body |
| 126025 | cg08293531 | -0.1206 | 0.0276 | 1.25e-05 | —- | 0.1038536 | 1.0000000 | chr15 | 101601180 | LRRK1 | Body |
| 48009 | cg03004999 | -0.0716 | 0.0164 | 1.27e-05 | —- | 0.1038536 | 1.0000000 | chr7 | 43152125 | HECW1 | TSS200 |
| 80568 | cg05169951 | 0.1712 | 0.0393 | 1.31e-05 | ++++ | 0.1051766 | 1.0000000 | chr16 | 3017955 | KREMEN2;PAQR4;KREMEN2 | Body;TSS1500;Body |
| 147224 | cg09845489 | 0.2281 | 0.0527 | 1.48e-05 | ++++ | 0.1130573 | 1.0000000 | chr7 | 157667853 | PTPRN2;PTPRN2;PTPRN2 | Body;Body;Body |
| 156274 | cg10502904 | 0.1329 | 0.0307 | 1.50e-05 | ++++ | 0.1130573 | 1.0000000 | chr10 | 131565289 | MGMT | 3’UTR |
| 90548 | cg05872129 | 0.5015 | 0.1159 | 1.50e-05 | ++++ | 0.1130573 | 1.0000000 | chr22 | 39784769 | ||
| 292637 | cg20923605 | 0.2592 | 0.0599 | 1.53e-05 | ++++ | 0.1130573 | 1.0000000 | chr13 | 112978683 | ||
| 265757 | cg18716164 | 0.1169 | 0.0271 | 1.58e-05 | ++++ | 0.1145115 | 1.0000000 | chr19 | 30019647 | VSTM2B | Body |
| 335850 | cg24454243 | -0.1659 | 0.0385 | 1.61e-05 | —- | 0.1148125 | 1.0000000 | chr7 | 105221985 | EFCAB10 | TSS200 |
| 38724 | cg02415779 | 0.1107 | 0.0257 | 1.64e-05 | -++- | 0.1148125 | 1.0000000 | chr22 | 18527778 | ||
| 349119 | cg25499746 | 0.0767 | 0.0179 | 1.77e-05 | +++- | 0.1217128 | 1.0000000 | chr6 | 16346054 | ATXN1;ATXN1 | 5’UTR;5’UTR |
| 219405 | cg15083015 | 0.1789 | 0.0417 | 1.82e-05 | ++++ | 0.1226391 | 1.0000000 | chr11 | 20625714 | SLC6A5 | Body |
| 339775 | cg24748746 | -0.2074 | 0.0485 | 1.86e-05 | —- | 0.1232680 | 1.0000000 | chr7 | 155738916 | ||
| 9019 | cg00534624 | 0.2244 | 0.0525 | 1.94e-05 | ++++ | 0.1239502 | 1.0000000 | chr16 | 1845096 | IGFALS;IGFALS;IGFALS | TSS200;TSS1500;TSS1500 |
| 91411 | cg05926928 | 0.4655 | 0.1090 | 1.94e-05 | ++++ | 0.1239502 | 1.0000000 | chr17 | 57297772 | GDPD1;GDPD1;GDPD1 | TSS200;TSS200;TSS200 |
| 95795 | cg06239191 | 0.1902 | 0.0447 | 2.08e-05 | ++++ | 0.1256788 | 1.0000000 | chr8 | 145163136 | KIAA1875 | Body |
| 370181 | cg27121095 | 0.1067 | 0.0251 | 2.09e-05 | -+++ | 0.1256788 | 1.0000000 | chr18 | 77155145 | NFATC1;NFATC1;NFATC1 | TSS1500;TSS1500;TSS1500 |
| 194801 | cg13483984 | 0.1031 | 0.0243 | 2.13e-05 | +++- | 0.1256788 | 1.0000000 | chr1 | 224580455 | WDR26;WDR26 | Body;Body |
| 153889 | cg10322744 | 0.4052 | 0.0953 | 2.14e-05 | ++++ | 0.1256788 | 1.0000000 | chr12 | 98910138 | TMPO;TMPO;TMPO;LOC100128191 | Body;Body;Body;TSS200 |
| 329980 | cg23990236 | 0.1203 | 0.0283 | 2.16e-05 | -+++ | 0.1256788 | 1.0000000 | chr1 | 12220146 | ||
| 259615 | cg18228116 | 0.2965 | 0.0700 | 2.27e-05 | -+++ | 0.1256788 | 1.0000000 | chr10 | 133995345 | JAKMIP3 | 3’UTR |
| 128672 | cg08487455 | 0.1474 | 0.0348 | 2.29e-05 | ++++ | 0.1256788 | 1.0000000 | chr16 | 76311050 | CNTNAP4 | TSS200 |
| 131033 | cg08654960 | -0.1347 | 0.0319 | 2.36e-05 | —- | 0.1256788 | 1.0000000 | chr16 | 85319859 | ||
| 12204 | cg00729699 | -0.0920 | 0.0218 | 2.36e-05 | —- | 0.1256788 | 1.0000000 | chr8 | 21918075 | EPB49;EPB49;EPB49;EPB49;EPB49;EPB49 | 5’UTR;5’UTR;5’UTR;5’UTR;5’UTR;5’UTR |
| 235393 | cg16353272 | 0.0828 | 0.0196 | 2.36e-05 | ++++ | 0.1256788 | 1.0000000 | chr16 | 2124240 | TSC2;TSC2;TSC2 | Body;Body;Body |
| 91432 | cg05927817 | 0.3361 | 0.0795 | 2.36e-05 | ++++ | 0.1256788 | 1.0000000 | chr6 | 18020357 | ||
| 80361 | cg05157266 | 0.1310 | 0.0310 | 2.38e-05 | +++- | 0.1256788 | 1.0000000 | chr2 | 183901614 | NCKAP1;NCKAP1 | Body;Body |
| 193732 | cg13423098 | 0.1356 | 0.0321 | 2.40e-05 | +++- | 0.1256788 | 1.0000000 | chr15 | 23807234 | ||
| 277830 | cg19702802 | 0.1563 | 0.0370 | 2.46e-05 | ++++ | 0.1262596 | 1.0000000 | chr19 | 46417729 | NANOS2 | 1stExon |
| 159378 | cg10729167 | 0.1354 | 0.0321 | 2.48e-05 | ++++ | 0.1262596 | 1.0000000 | chr10 | 111220101 | ||
| 337433 | cg24577193 | -0.3193 | 0.0759 | 2.57e-05 | —- | 0.1274285 | 1.0000000 | chr1 | 78148396 | ZZZ3 | TSS200 |
| 269647 | cg19029220 | -0.0802 | 0.0191 | 2.61e-05 | +— | 0.1274285 | 1.0000000 | chr2 | 64067822 | UGP2;UGP2 | TSS1500;TSS1500 |
| 321501 | cg23313031 | -0.0993 | 0.0236 | 2.63e-05 | —- | 0.1274285 | 1.0000000 | chr6 | 29974745 | HLA-J;NCRNA00171 | Body;Body |
| 320947 | cg23268677 | 0.2321 | 0.0552 | 2.63e-05 | ++++ | 0.1274285 | 1.0000000 | chr22 | 19929097 | TXNRD2;COMT | Body;TSS200 |
| 196530 | cg13587236 | 0.0881 | 0.0210 | 2.71e-05 | +++- | 0.1294457 | 1.0000000 | chr9 | 128472496 | ||
| 64158 | cg04080724 | 0.1031 | 0.0246 | 2.82e-05 | ++++ | 0.1327804 | 1.0000000 | chr4 | 140202327 | C4orf49 | TSS1500 |
| 162593 | cg10980774 | 0.1419 | 0.0341 | 3.12e-05 | ++++ | 0.1450755 | 1.0000000 | chr11 | 112832547 | NCAM1;NCAM1;NCAM1 | Body;Body;Body |
| 4028 | cg00238318 | -0.1141 | 0.0274 | 3.18e-05 | –+- | 0.1450755 | 1.0000000 | chr10 | 94607950 | EXOC6;EXOC6 | Body;TSS1500 |
| 39898 | cg02492873 | 0.1026 | 0.0247 | 3.19e-05 | ++– | 0.1450755 | 1.0000000 | chr2 | 25193821 | DNAJC27 | Body |
| 348207 | cg25423077 | 0.3801 | 0.0915 | 3.26e-05 | ++++ | 0.1463134 | 1.0000000 | chr18 | 59221601 | CDH20 | Body |
| 338787 | cg24682751 | -0.1872 | 0.0451 | 3.36e-05 | —- | 0.1488781 | 1.0000000 | chr15 | 93591750 | RGMA;RGMA;RGMA;RGMA;RGMA;RGMA | Body;Body;Body;Body;Body;Body |
| 190991 | cg13221086 | 0.0873 | 0.0211 | 3.39e-05 | +++- | 0.1488781 | 1.0000000 | chr3 | 31809318 | OSBPL10 | Body |
| 95484 | cg06216157 | -0.0646 | 0.0156 | 3.47e-05 | –+- | 0.1506368 | 1.0000000 | chr17 | 7210363 | EIF5A;EIF5A;EIF5A;EIF5A;EIF5A | TSS1500;5’UTR;TSS1500;TSS1500;1stExon |
| 179110 | cg12235073 | 0.1005 | 0.0243 | 3.57e-05 | ++++ | 0.1528272 | 1.0000000 | chr10 | 6270423 | PFKFB3;PFKFB3 | Body;Body |
| 167176 | cg11332363 | 0.1782 | 0.0431 | 3.64e-05 | ++-+ | 0.1528272 | 1.0000000 | chr19 | 54023999 | ZNF331 | TSS200 |
| 304836 | cg21936789 | 0.1721 | 0.0417 | 3.64e-05 | ++++ | 0.1528272 | 1.0000000 | chr3 | 47620545 | CSPG5 | TSS200 |
| 5926 | cg00353112 | -0.0979 | 0.0238 | 3.82e-05 | —- | 0.1570929 | 1.0000000 | chr15 | 45879221 | PLDN | TSS200 |
| 69221 | cg04406454 | -0.1479 | 0.0359 | 3.83e-05 | —- | 0.1570929 | 1.0000000 | chr6 | 10398494 | TFAP2A;TFAP2A;TFAP2A | 3’UTR;3’UTR;3’UTR |
| 110491 | cg07219314 | -0.1410 | 0.0343 | 3.88e-05 | —- | 0.1573107 | 1.0000000 | chr22 | 23744725 | ZDHHC8P | Body |
| 295936 | cg21185289 | 0.2772 | 0.0675 | 4.02e-05 | ++++ | 0.1613376 | 1.0000000 | chr2 | 74743437 | TLX2 | 3’UTR |
| 107294 | cg07019740 | 0.2793 | 0.0681 | 4.07e-05 | ++++ | 0.1616651 | 1.0000000 | chr22 | 19929205 | TXNRD2;COMT | Body;TSS200 |
| 362881 | cg26580480 | -0.0960 | 0.0234 | 4.18e-05 | —- | 0.1643442 | 1.0000000 | chr6 | 43241339 | TTBK1 | Body |
| 229928 | cg15931233 | 0.0783 | 0.0191 | 4.34e-05 | ++++ | 0.1680165 | 1.0000000 | chr5 | 53455496 | ARL15 | Body |
| 135334 | cg08963616 | 0.0861 | 0.0211 | 4.37e-05 | ++++ | 0.1680165 | 1.0000000 | chr8 | 17249585 | MTMR7 | Body |
| 59640 | cg03770962 | 0.0905 | 0.0221 | 4.41e-05 | +++- | 0.1680165 | 1.0000000 | chr7 | 148477754 | CUL1 | Body |
| 87925 | cg05677467 | 0.0620 | 0.0152 | 4.50e-05 | ++-+ | 0.1698457 | 1.0000000 | chr15 | 85197654 | WDR73 | TSS200 |
| X | ONTOLOGY | TERM | N | DE | P.DE | FDR |
|---|---|---|---|---|---|---|
| GO:0034156 | BP | negative regulation of toll-like receptor 7 signaling pathway | 1 | 1 | 0.0006729 | 1 |
| GO:0004325 | MF | ferrochelatase activity | 1 | 1 | 0.0008725 | 1 |
| GO:0042053 | BP | regulation of dopamine metabolic process | 18 | 2 | 0.0013589 | 1 |
| GO:0042069 | BP | regulation of catecholamine metabolic process | 18 | 2 | 0.0013589 | 1 |
| GO:0048609 | BP | multicellular organismal reproductive process | 753 | 6 | 0.0016644 | 1 |
| GO:0032504 | BP | multicellular organism reproduction | 768 | 6 | 0.0017622 | 1 |
| GO:0032997 | CC | Fc receptor complex | 3 | 1 | 0.0019011 | 1 |
| GO:0032998 | CC | Fc-epsilon receptor I complex | 3 | 1 | 0.0019011 | 1 |
| GO:0034155 | BP | regulation of toll-like receptor 7 signaling pathway | 3 | 1 | 0.0019833 | 1 |
| GO:0042417 | BP | dopamine metabolic process | 33 | 2 | 0.0038976 | 1 |
| GO:0031337 | BP | positive regulation of sulfur amino acid metabolic process | 1 | 1 | 0.0048329 | 1 |
| GO:0050668 | BP | positive regulation of homocysteine metabolic process | 1 | 1 | 0.0048329 | 1 |
| GO:1904527 | BP | negative regulation of microtubule binding | 2 | 1 | 0.0049443 | 1 |
| GO:0050666 | BP | regulation of homocysteine metabolic process | 2 | 1 | 0.0055603 | 1 |
| GO:1902816 | BP | regulation of protein localization to microtubule | 5 | 1 | 0.0055794 | 1 |
| GO:1902817 | BP | negative regulation of protein localization to microtubule | 5 | 1 | 0.0055794 | 1 |
| GO:0051267 | MF | CP2 mannose-ethanolamine phosphotransferase activity | 1 | 1 | 0.0057471 | 1 |
| GO:0072299 | BP | negative regulation of metanephric glomerulus development | 1 | 1 | 0.0058507 | 1 |
| GO:0072302 | BP | negative regulation of metanephric glomerular mesangial cell proliferation | 1 | 1 | 0.0058507 | 1 |
| GO:0006584 | BP | catecholamine metabolic process | 46 | 2 | 0.0058803 | 1 |
| GO:0009712 | BP | catechol-containing compound metabolic process | 46 | 2 | 0.0058803 | 1 |
| GO:0008502 | MF | melatonin receptor activity | 3 | 1 | 0.0059440 | 1 |
| GO:0001544 | BP | initiation of primordial ovarian follicle growth | 2 | 1 | 0.0062992 | 1 |
| GO:0031335 | BP | regulation of sulfur amino acid metabolic process | 3 | 1 | 0.0063248 | 1 |
| GO:0016036 | BP | cellular response to phosphate starvation | 2 | 1 | 0.0064527 | 1 |
| GO:0034154 | BP | toll-like receptor 7 signaling pathway | 6 | 1 | 0.0069035 | 1 |
| GO:0016209 | MF | antioxidant activity | 83 | 2 | 0.0069530 | 1 |
| GO:0021935 | BP | cerebellar granule cell precursor tangential migration | 2 | 1 | 0.0070459 | 1 |
| GO:0016206 | MF | catechol O-methyltransferase activity | 2 | 1 | 0.0071794 | 1 |
| GO:0102084 | MF | L-dopa O-methyltransferase activity | 2 | 1 | 0.0071794 | 1 |
| GO:0102938 | MF | orcinol O-methyltransferase activity | 2 | 1 | 0.0071794 | 1 |
| GO:0072301 | BP | regulation of metanephric glomerular mesangial cell proliferation | 2 | 1 | 0.0072438 | 1 |
| GO:0051377 | MF | mannose-ethanolamine phosphotransferase activity | 3 | 1 | 0.0072565 | 1 |
| GO:0045764 | BP | positive regulation of cellular amino acid metabolic process | 3 | 1 | 0.0074539 | 1 |
| GO:0042698 | BP | ovulation cycle | 69 | 2 | 0.0075994 | 1 |
| GO:0035814 | BP | negative regulation of renal sodium excretion | 3 | 1 | 0.0078159 | 1 |
| GO:0061032 | BP | visceral serous pericardium development | 2 | 1 | 0.0078660 | 1 |
| GO:0033238 | BP | regulation of cellular amine metabolic process | 78 | 2 | 0.0080612 | 1 |
| GO:0046501 | BP | protoporphyrinogen IX metabolic process | 10 | 1 | 0.0081033 | 1 |
| GO:0004416 | MF | hydroxyacylglutathione hydrolase activity | 2 | 1 | 0.0083624 | 1 |
| GO:0019243 | BP | methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione | 2 | 1 | 0.0083624 | 1 |
| GO:0051596 | BP | methylglyoxal catabolic process | 2 | 1 | 0.0083624 | 1 |
| GO:0061727 | BP | methylglyoxal catabolic process to lactate | 2 | 1 | 0.0083624 | 1 |
| GO:0072262 | BP | metanephric glomerular mesangial cell proliferation involved in metanephros development | 3 | 1 | 0.0088988 | 1 |
| GO:0051176 | BP | positive regulation of sulfur metabolic process | 3 | 1 | 0.0090728 | 1 |
| GO:0072166 | BP | posterior mesonephric tubule development | 2 | 1 | 0.0095614 | 1 |
| GO:0021934 | BP | hindbrain tangential cell migration | 3 | 1 | 0.0097382 | 1 |
| GO:0070181 | MF | small ribosomal subunit rRNA binding | 10 | 1 | 0.0101955 | 1 |
| GO:0035801 | BP | adrenal cortex development | 2 | 1 | 0.0103000 | 1 |
| GO:0035802 | BP | adrenal cortex formation | 2 | 1 | 0.0103000 | 1 |
| GO:0098869 | BP | cellular oxidant detoxification | 96 | 2 | 0.0105889 | 1 |
| GO:2001074 | BP | regulation of metanephric ureteric bud development | 2 | 1 | 0.0107573 | 1 |
| GO:2001076 | BP | positive regulation of metanephric ureteric bud development | 2 | 1 | 0.0107573 | 1 |
| GO:1990748 | BP | cellular detoxification | 105 | 2 | 0.0114517 | 1 |
| GO:1905643 | BP | positive regulation of DNA methylation | 3 | 1 | 0.0119423 | 1 |
| GO:0016013 | CC | syntrophin complex | 3 | 1 | 0.0122287 | 1 |
| GO:1903527 | BP | positive regulation of membrane tubulation | 4 | 1 | 0.0122956 | 1 |
| GO:0034164 | BP | negative regulation of toll-like receptor 9 signaling pathway | 3 | 1 | 0.0125471 | 1 |
| GO:0009438 | BP | methylglyoxal metabolic process | 5 | 1 | 0.0125610 | 1 |
| GO:0032687 | BP | negative regulation of interferon-alpha production | 6 | 1 | 0.0126305 | 1 |
| GO:0044729 | MF | hemi-methylated DNA-binding | 3 | 1 | 0.0131488 | 1 |
| GO:0042420 | BP | dopamine catabolic process | 5 | 1 | 0.0131948 | 1 |
| GO:0010385 | MF | double-stranded methylated DNA binding | 4 | 1 | 0.0132070 | 1 |
| GO:0044106 | BP | cellular amine metabolic process | 119 | 2 | 0.0137636 | 1 |
| GO:0042182 | BP | ketone catabolic process | 9 | 1 | 0.0140733 | 1 |
| GO:0071535 | MF | RING-like zinc finger domain binding | 4 | 1 | 0.0142495 | 1 |
| GO:0036353 | BP | histone H2A-K119 monoubiquitination | 8 | 1 | 0.0144099 | 1 |
| GO:0072223 | BP | metanephric glomerular mesangium development | 5 | 1 | 0.0144316 | 1 |
| GO:2000195 | BP | negative regulation of female gonad development | 5 | 1 | 0.0144413 | 1 |
| GO:0045914 | BP | negative regulation of catecholamine metabolic process | 4 | 1 | 0.0147543 | 1 |
| GO:0045963 | BP | negative regulation of dopamine metabolic process | 4 | 1 | 0.0147543 | 1 |
| GO:1903525 | BP | regulation of membrane tubulation | 6 | 1 | 0.0153190 | 1 |
| GO:0009308 | BP | amine metabolic process | 128 | 2 | 0.0153320 | 1 |
| GO:0072125 | BP | negative regulation of glomerular mesangial cell proliferation | 4 | 1 | 0.0154115 | 1 |
| GO:0090194 | BP | negative regulation of glomerulus development | 4 | 1 | 0.0154115 | 1 |
| GO:0019614 | BP | catechol-containing compound catabolic process | 6 | 1 | 0.0155222 | 1 |
| GO:0042424 | BP | catecholamine catabolic process | 6 | 1 | 0.0155222 | 1 |
| GO:0098754 | BP | detoxification | 129 | 2 | 0.0158916 | 1 |
| GO:0007356 | BP | thorax and anterior abdomen determination | 5 | 1 | 0.0168477 | 1 |
| GO:0007614 | BP | short-term memory | 9 | 1 | 0.0176631 | 1 |
| GO:0001547 | BP | antral ovarian follicle growth | 8 | 1 | 0.0178660 | 1 |
| GO:0008585 | BP | female gonad development | 92 | 2 | 0.0180206 | 1 |
| GO:0034163 | BP | regulation of toll-like receptor 9 signaling pathway | 8 | 1 | 0.0185349 | 1 |
| GO:0044703 | BP | multi-organism reproductive process | 911 | 5 | 0.0185365 | 1 |
| GO:1905940 | BP | negative regulation of gonad development | 6 | 1 | 0.0186027 | 1 |
| GO:0019336 | BP | phenol-containing compound catabolic process | 9 | 1 | 0.0187532 | 1 |
| GO:0072298 | BP | regulation of metanephric glomerulus development | 5 | 1 | 0.0188366 | 1 |
| GO:0046185 | BP | aldehyde catabolic process | 11 | 1 | 0.0190056 | 1 |
| GO:0035502 | BP | metanephric part of ureteric bud development | 6 | 1 | 0.0190321 | 1 |
| GO:0004791 | MF | thioredoxin-disulfide reductase activity | 7 | 1 | 0.0191359 | 1 |
| GO:0051537 | MF | 2 iron, 2 sulfur cluster binding | 21 | 1 | 0.0194764 | 1 |
| GO:0018958 | BP | phenol-containing compound metabolic process | 94 | 2 | 0.0196449 | 1 |
| GO:0046545 | BP | development of primary female sexual characteristics | 96 | 2 | 0.0201548 | 1 |
| GO:0033240 | BP | positive regulation of cellular amine metabolic process | 7 | 1 | 0.0210294 | 1 |
| GO:0016668 | MF | oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor | 11 | 1 | 0.0220457 | 1 |
| GO:0072284 | BP | metanephric S-shaped body morphogenesis | 6 | 1 | 0.0220657 | 1 |
| GO:0048511 | BP | rhythmic process | 286 | 3 | 0.0222464 | 1 |
| GO:0007354 | BP | zygotic determination of anterior/posterior axis, embryo | 6 | 1 | 0.0227852 | 1 |
| GO:0035372 | BP | protein localization to microtubule | 14 | 1 | 0.0228225 | 1 |
| GO:0033239 | BP | negative regulation of cellular amine metabolic process | 7 | 1 | 0.0229552 | 1 |
metal_blood_cell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/blood_cell_common_DVP_1204201.tbl', sep = "\t")
metal_blood_cell_DVP = metalProcess(metal_blood_cell_DVP)
write.csv(metal_blood_cell_DVP, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DVP_blood_cell_common_120420.csv')
# Significant probes
# Nominal P-value
table(metal_blood_cell_DVP$P.value < 0.05)
# FALSE TRUE
# 348773 28578
# FDR
table(metal_blood_cell_DVP$P.FDR < 0.05)
# FALSE TRUE
# 377328 23
table(metal_blood_cell_DVP$P.FDR < 0.1)
# FALSE TRUE
# 377266 85
# Bonferroni
table(metal_blood_cell_DVP$P.Bonf < 0.05)
# FALSE TRUE
# 377347 4
# GO analysis, FDR < 0.1 probes
go_metal_blood_cell_DVP = gometh(sig.cpg = metal_blood_cell_DVP$Name[metal_blood_cell_DVP$P.FDR < 0.1], all.cpg = metal_blood_cell_DVP$Name, array.type = '450K', anno = annAll2)
go_metal_blood_cell_DVP = go_metal_blood_cell_DVP[order(go_metal_blood_cell_DVP$P.DE),]
table(go_metal_blood_cell_DVP$P.DE<0.05)
# FALSE TRUE
# 22282 301
table(go_metal_blood_cell_DVP$FDR<0.05)
# FALSE
# 22583
write.csv(go_metal_blood_cell_DVP[go_metal_blood_cell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DVP_blood_cell_common_120420.csv')
# KEGG analysis, FDR < 0.1 probes
kegg_metal_blood_cell_DVP = gometh(sig.cpg = metal_blood_cell_DVP$Name[metal_blood_cell_DVP$P.FDR < 0.1], all.cpg = metal_blood_cell_DVP$Name, array.type = '450K', collection = 'KEGG', sig.genes = T, anno = annAll2)
kegg_metal_blood_cell_DVP = kegg_metal_blood_cell_DVP[order(kegg_metal_blood_cell_DVP$P.DE),]
table(kegg_metal_blood_cell_DVP$P.DE<0.05)
# FALSE TRUE
# 335 5
table(kegg_metal_blood_cell_DVP$FDR<0.05)
# FALSE
# 340
write.csv(kegg_metal_blood_cell_DVP[kegg_metal_blood_cell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DVP_blood_cell_common_120420.csv')
# Plotting
gg_qqplot(metal_blood_cell_DVP$P.value)
quartz.save('qq_metal_blood_cell_DVP_120420.png', type = "png", dpi = 300)
manhattan_meta(metal_blood_cell_DVP, FDR=T)
quartz.save('manhattan_metal_blood_cell_DVP_120420.png', type = "png", dpi = 300)
volcano_meta(metal_blood_cell_DVP, FDR = TRUE)
quartz.save('volcano_metal_blood_cell_DVP_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_blood_cell_DVP_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_blood_cell_DVP_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_blood_cell_DVP_120420.png")
| X | Name | Effect | StdErr | P.value | Direction | P.FDR | P.Bonf | chr | pos | UCSC_RefGene_Name | UCSC_RefGene_Group |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 321132 | cg23281729 | 0.9728 | 0.1462 | 0.00e+00 | -++ | 0.0000108 | 0.0000108 | chr18 | 78005477 | PARD6G | TSS200 |
| 374163 | cg27425262 | 0.8238 | 0.1473 | 0.00e+00 | +++ | 0.0042584 | 0.0085168 | chr2 | 113953981 | PSD4;LOC440839 | Body;Body |
| 167567 | cg11361658 | 0.1740 | 0.0323 | 1.00e-07 | +++ | 0.0087332 | 0.0261995 | chr5 | 128452311 | ||
| 50934 | cg03205258 | 0.6862 | 0.1287 | 1.00e-07 | +++ | 0.0091725 | 0.0366898 | chr22 | 19929274 | TXNRD2;COMT;COMT | 1stExon;1stExon;5’UTR |
| 145256 | cg09692492 | -0.3502 | 0.0664 | 1.00e-07 | — | 0.0102489 | 0.0512443 | chr22 | 23744717 | ZDHHC8P | Body |
| 163279 | cg11032634 | 0.7694 | 0.1503 | 3.00e-07 | +++ | 0.0192135 | 0.1152807 | chr22 | 19929254 | TXNRD2;COMT | 1stExon;TSS200 |
| 237588 | cg16511076 | 0.1302 | 0.0257 | 4.00e-07 | +++ | 0.0219295 | 0.1535064 | chr4 | 48887480 | OCIAD2;OCIAD2 | 3’UTR;3’UTR |
| 309909 | cg22387890 | 0.5501 | 0.1098 | 5.00e-07 | +++ | 0.0228562 | 0.2051280 | chr7 | 6145595 | USP42 | 5’UTR |
| 314099 | cg22749736 | 0.1312 | 0.0262 | 6.00e-07 | +++ | 0.0228562 | 0.2087506 | chr11 | 1306759 | TOLLIP | Body |
| 64158 | cg04080724 | 0.1387 | 0.0278 | 6.00e-07 | +++ | 0.0228562 | 0.2285615 | chr4 | 140202327 | C4orf49 | TSS1500 |
| 80568 | cg05169951 | 0.2307 | 0.0465 | 7.00e-07 | +++ | 0.0239892 | 0.2638816 | chr16 | 3017955 | KREMEN2;PAQR4;KREMEN2 | Body;TSS1500;Body |
| 11224 | cg00668103 | 0.1440 | 0.0292 | 8.00e-07 | +++ | 0.0254209 | 0.3050505 | chr7 | 100084730 | C7orf51 | Body |
| 124685 | cg08207566 | 0.1245 | 0.0255 | 1.00e-06 | +++ | 0.0303042 | 0.3939544 | chr4 | 174086461 | ||
| 18303 | cg01101647 | 0.1337 | 0.0275 | 1.10e-06 | +++ | 0.0303228 | 0.4245199 | chr4 | 66535732 | EPHA5;EPHA5 | TSS200;TSS200 |
| 116190 | cg07611790 | 0.1053 | 0.0217 | 1.30e-06 | +++ | 0.0309847 | 0.4724435 | chr19 | 49240823 | RASIP1 | Body |
| 171628 | cg11691429 | 0.2056 | 0.0426 | 1.40e-06 | +++ | 0.0309847 | 0.5248952 | chr2 | 947634 | SNTG2 | Body |
| 295936 | cg21185289 | 0.3802 | 0.0789 | 1.50e-06 | +++ | 0.0309847 | 0.5471590 | chr2 | 74743437 | TLX2 | 3’UTR |
| 125889 | cg08285768 | 0.1113 | 0.0231 | 1.50e-06 | +++ | 0.0309847 | 0.5577248 | chr15 | 86038622 | AKAP13;AKAP13 | Body;Body |
| 202666 | cg13972353 | 0.1460 | 0.0304 | 1.60e-06 | +++ | 0.0311811 | 0.5924411 | chr9 | 139354348 | SEC16A | Body |
| 102811 | cg06740986 | 0.1067 | 0.0225 | 2.10e-06 | +++ | 0.0392634 | 0.7852674 | chr1 | 184838417 | FAM129A | Body |
| 303849 | cg21857098 | 0.1220 | 0.0259 | 2.50e-06 | +++ | 0.0428636 | 0.9286608 | chr15 | 25638137 | UBE3A;UBE3A;UBE3A | Body;Body;Body |
| 55105 | cg03479942 | 0.1266 | 0.0269 | 2.50e-06 | +++ | 0.0428636 | 0.9430001 | chr16 | 69341763 | SNTB2 | 3’UTR |
| 121453 | cg07984508 | 0.1050 | 0.0224 | 2.70e-06 | +++ | 0.0447243 | 1.0000000 | chr15 | 77426719 | SGK269 | Body |
| 168599 | cg11440940 | 0.1144 | 0.0246 | 3.30e-06 | +++ | 0.0509569 | 1.0000000 | chr19 | 8510764 | HNRNPM;HNRNPM | Body;Body |
| 150964 | cg10117884 | 0.1325 | 0.0285 | 3.40e-06 | +++ | 0.0509569 | 1.0000000 | chr1 | 166955898 | ||
| 308533 | cg22267402 | 0.1390 | 0.0300 | 3.50e-06 | +++ | 0.0509569 | 1.0000000 | chr22 | 44463707 | PARVB;PARVB | Body;Body |
| 100415 | cg06581201 | 0.2001 | 0.0434 | 4.00e-06 | +++ | 0.0529265 | 1.0000000 | chr6 | 168534038 | ||
| 248409 | cg17332762 | 0.1085 | 0.0236 | 4.20e-06 | +++ | 0.0529265 | 1.0000000 | chr3 | 106967639 | LOC344595;LOC344595 | Body;Body |
| 93087 | cg06039392 | 0.1497 | 0.0325 | 4.20e-06 | +++ | 0.0529265 | 1.0000000 | chr4 | 187476953 | MTNR1A | TSS1500 |
| 58507 | cg03700279 | 0.1118 | 0.0243 | 4.20e-06 | +++ | 0.0529265 | 1.0000000 | chr2 | 44576358 | PREPL;PREPL;PREPL;PREPL;PREPL;PREPL;PREPL | Body;Body;5’UTR;5’UTR;Body;Body;Body |
| 32578 | cg02026246 | 0.1671 | 0.0364 | 4.30e-06 | +++ | 0.0529265 | 1.0000000 | chr11 | 22687589 | GAS2 | TSS1500 |
| 373469 | cg27371984 | 0.2504 | 0.0547 | 4.80e-06 | +++ | 0.0561545 | 1.0000000 | chr17 | 78009155 | CCDC40;TBC1D16 | TSS1500;5’UTR |
| 156274 | cg10502904 | 0.1806 | 0.0396 | 5.10e-06 | +++ | 0.0582035 | 1.0000000 | chr10 | 131565289 | MGMT | 3’UTR |
| 208658 | cg14332223 | 0.1916 | 0.0421 | 5.30e-06 | –+ | 0.0592108 | 1.0000000 | chr19 | 56136067 | ZNF784 | TSS200 |
| 129911 | cg08575722 | -0.1446 | 0.0318 | 5.50e-06 | — | 0.0595244 | 1.0000000 | chr11 | 32421845 | WT1;WT1;WT1;WT1 | Body;Body;Body;Body |
| 120767 | cg07935287 | -0.1377 | 0.0304 | 5.80e-06 | — | 0.0605019 | 1.0000000 | chr18 | 54318347 | WDR7;WDR7 | TSS1500;TSS1500 |
| 25526 | cg01570086 | -0.1467 | 0.0325 | 6.20e-06 | — | 0.0633032 | 1.0000000 | chr15 | 74833080 | ARID3B | TSS1500 |
| 110491 | cg07219314 | -0.1929 | 0.0428 | 6.60e-06 | — | 0.0645540 | 1.0000000 | chr22 | 23744725 | ZDHHC8P | Body |
| 199880 | cg13797228 | 0.1106 | 0.0246 | 7.00e-06 | -++ | 0.0645540 | 1.0000000 | chr3 | 126076243 | KLF15 | TSS200 |
| 214646 | cg14718822 | -0.1749 | 0.0389 | 7.10e-06 | -+- | 0.0645540 | 1.0000000 | chr6 | 84234250 | PRSS35;PRSS35 | Body;Body |
| 156000 | cg10485752 | 0.1511 | 0.0337 | 7.20e-06 | +++ | 0.0645540 | 1.0000000 | chr1 | 26021655 | MAN1C1 | Body |
| 109701 | cg07168204 | 0.1274 | 0.0284 | 7.20e-06 | +++ | 0.0645540 | 1.0000000 | chr5 | 149864599 | ||
| 10618 | cg00629117 | 0.7703 | 0.1719 | 7.40e-06 | +++ | 0.0650448 | 1.0000000 | chr16 | 1844932 | IGFALS;IGFALS;IGFALS | TSS200;TSS1500;TSS1500 |
| 11047 | cg00657529 | 0.0977 | 0.0219 | 8.00e-06 | +++ | 0.0684034 | 1.0000000 | chr6 | 31698687 | CLIC1;DDAH2 | Body;TSS1500 |
| 227727 | cg15754901 | 0.1165 | 0.0261 | 8.30e-06 | +-+ | 0.0692900 | 1.0000000 | chr17 | 5402972 | LOC728392 | 3’UTR |
| 320947 | cg23268677 | 0.3213 | 0.0723 | 8.70e-06 | +++ | 0.0717705 | 1.0000000 | chr22 | 19929097 | TXNRD2;COMT | Body;TSS200 |
| 293675 | cg21004290 | 0.1299 | 0.0293 | 9.00e-06 | +++ | 0.0719697 | 1.0000000 | chr8 | 131250320 | ASAP1 | Body |
| 324700 | cg23574838 | 0.0719 | 0.0163 | 1.01e-05 | +++ | 0.0778535 | 1.0000000 | chr20 | 3186475 | DDRGK1 | TSS1500 |
| 132616 | cg08770961 | 0.3268 | 0.0741 | 1.03e-05 | +++ | 0.0778535 | 1.0000000 | chr16 | 66956122 | RRAD;RRAD | Body;Body |
| 316511 | cg22938135 | 0.0961 | 0.0218 | 1.06e-05 | +++ | 0.0778535 | 1.0000000 | chr5 | 175841493 | CLTB;CLTB | Body;Body |
| 107264 | cg07018132 | 0.0975 | 0.0222 | 1.10e-05 | +++ | 0.0778535 | 1.0000000 | chr16 | 718091 | RHOT2 | TSS200 |
| 281026 | cg19929852 | 0.1226 | 0.0279 | 1.10e-05 | +++ | 0.0778535 | 1.0000000 | chr4 | 15068643 | CPEB2;CPEB2 | 3’UTR;3’UTR |
| 351734 | cg25721832 | 0.0929 | 0.0212 | 1.12e-05 | +++ | 0.0778535 | 1.0000000 | chr3 | 81913557 | ||
| 268961 | cg18971529 | 0.3043 | 0.0693 | 1.15e-05 | ++- | 0.0778535 | 1.0000000 | chr21 | 30391563 | RWDD2B | 1stExon |
| 198387 | cg13698261 | 0.1019 | 0.0232 | 1.15e-05 | +++ | 0.0778535 | 1.0000000 | chr9 | 97841956 | C9orf3 | Body |
| 109543 | cg07159858 | -0.1358 | 0.0310 | 1.16e-05 | +– | 0.0778535 | 1.0000000 | chr14 | 75744601 | FOS | TSS1500 |
| 62770 | cg03988518 | 0.1819 | 0.0415 | 1.18e-05 | ++- | 0.0778535 | 1.0000000 | chr6 | 170763536 | ||
| 149284 | cg09996597 | 0.4310 | 0.0985 | 1.22e-05 | +++ | 0.0781745 | 1.0000000 | chr16 | 1844927 | IGFALS;IGFALS;IGFALS | TSS200;TSS1500;TSS1500 |
| 51985 | cg03277137 | 0.0799 | 0.0183 | 1.22e-05 | +++ | 0.0781745 | 1.0000000 | chr13 | 113513653 | ATP11A;ATP11A | Body;Body |
| 120984 | cg07952047 | 0.1885 | 0.0431 | 1.24e-05 | +++ | 0.0781745 | 1.0000000 | chr19 | 54024110 | ZNF331 | TSS200 |
| 35145 | cg02192228 | 0.1987 | 0.0455 | 1.29e-05 | +++ | 0.0791857 | 1.0000000 | chr3 | 8809536 | OXTR | Body |
| 178342 | cg12175949 | 0.3943 | 0.0906 | 1.35e-05 | +++ | 0.0791857 | 1.0000000 | chr22 | 19929286 | TXNRD2;COMT;COMT | 1stExon;1stExon;5’UTR |
| 259615 | cg18228116 | 0.3740 | 0.0860 | 1.36e-05 | -++ | 0.0791857 | 1.0000000 | chr10 | 133995345 | JAKMIP3 | 3’UTR |
| 114654 | cg07510163 | 0.1646 | 0.0378 | 1.36e-05 | +++ | 0.0791857 | 1.0000000 | chr2 | 44547313 | PREPL;PREPL;PREPL;PREPL;PREPL;PREPL;SLC3A1;PREPL | 3’UTR;3’UTR;3’UTR;3’UTR;3’UTR;3’UTR;Body;3’UTR |
| 282819 | cg20074307 | 0.0870 | 0.0200 | 1.36e-05 | +++ | 0.0791857 | 1.0000000 | chr14 | 55092491 | SAMD4A;SAMD4A | Body;Body |
| 169144 | cg11494866 | 0.1107 | 0.0255 | 1.39e-05 | +++ | 0.0794152 | 1.0000000 | chr8 | 42695070 | THAP1;THAP1 | Body;Body |
| 271236 | cg19170881 | -0.1888 | 0.0435 | 1.42e-05 | — | 0.0802012 | 1.0000000 | chr7 | 101129980 | EMID2 | Body |
| 351392 | cg25691442 | 0.1096 | 0.0253 | 1.46e-05 | +++ | 0.0812969 | 1.0000000 | chr15 | 63345512 | TPM1;TPM1;TPM1;TPM1;TPM1;TPM1;TPM1 | Body;Body;Body;Body;Body;Body;Body |
| 138885 | cg09235788 | 0.1447 | 0.0335 | 1.57e-05 | +++ | 0.0859704 | 1.0000000 | chr1 | 111220207 | ||
| 370643 | cg27155653 | -0.1124 | 0.0261 | 1.61e-05 | — | 0.0867907 | 1.0000000 | chr1 | 183604774 | ARPC5;RGL1 | 1stExon;TSS1500 |
| 351214 | cg25674826 | 0.2883 | 0.0670 | 1.71e-05 | +++ | 0.0906705 | 1.0000000 | chr21 | 35446543 | MRPS6;SLC5A3 | Body;5’UTR |
| 148318 | cg09920145 | -0.1037 | 0.0241 | 1.76e-05 | — | 0.0923986 | 1.0000000 | chr3 | 69100714 | TMF1 | Body |
| 232066 | cg16101346 | 0.1755 | 0.0409 | 1.79e-05 | -++ | 0.0924251 | 1.0000000 | chr1 | 186650479 | PTGS2 | TSS1500 |
| 343712 | cg25052374 | 0.0833 | 0.0194 | 1.83e-05 | +++ | 0.0935728 | 1.0000000 | chr17 | 76991253 | CANT1;CANT1;CANT1 | Body;Body;Body |
| 207024 | cg14231959 | 0.1401 | 0.0327 | 1.90e-05 | +++ | 0.0940895 | 1.0000000 | chr8 | 1897035 | ARHGEF10 | Body |
| 222184 | cg15317815 | 0.2440 | 0.0570 | 1.90e-05 | +++ | 0.0940895 | 1.0000000 | chr3 | 8809306 | OXTR | Body |
| 349119 | cg25499746 | 0.0878 | 0.0205 | 1.94e-05 | +++ | 0.0949748 | 1.0000000 | chr6 | 16346054 | ATXN1;ATXN1 | 5’UTR;5’UTR |
| 114218 | cg07479711 | 0.1174 | 0.0275 | 1.98e-05 | +++ | 0.0953886 | 1.0000000 | chr5 | 1524940 | LPCAT1 | TSS1500 |
| 26498 | cg01632803 | 0.1085 | 0.0254 | 2.00e-05 | +++ | 0.0953886 | 1.0000000 | chr19 | 48891159 | KDELR1 | Body |
| 127440 | cg08400962 | 0.1223 | 0.0287 | 2.04e-05 | +++ | 0.0955490 | 1.0000000 | chr19 | 34112316 | CHST8;CHST8 | TSS1500;TSS1500 |
| 64658 | cg04111999 | 0.1037 | 0.0244 | 2.05e-05 | +++ | 0.0955490 | 1.0000000 | chr10 | 22615540 | BMI1 | Body |
| 265593 | cg18703721 | 0.1274 | 0.0299 | 2.10e-05 | +++ | 0.0966387 | 1.0000000 | chr10 | 75282672 | USP54 | Body |
| 41686 | cg02608453 | 0.1053 | 0.0248 | 2.20e-05 | +++ | 0.0986884 | 1.0000000 | chr9 | 125241447 | OR1J1 | TSS1500 |
| 161566 | cg10898607 | -0.1150 | 0.0271 | 2.20e-05 | — | 0.0986884 | 1.0000000 | chr3 | 101405733 | RPL24 | TSS200 |
| 377087 | cg27647852 | 0.0989 | 0.0233 | 2.22e-05 | +++ | 0.0986884 | 1.0000000 | chr20 | 44036899 | DBNDD2;DBNDD2;DBNDD2;SYS1-DBNDD2;DBNDD2;DBNDD2;DBNDD2 | 5’UTR;5’UTR;TSS200;Body;5’UTR;5’UTR;TSS200 |
| 181408 | cg12433479 | 0.1713 | 0.0405 | 2.38e-05 | +++ | 0.1031703 | 1.0000000 | chr3 | 38683662 | SCN5A;SCN5A;SCN5A;SCN5A;SCN5A;SCN5A | 5’UTR;5’UTR;5’UTR;5’UTR;5’UTR;5’UTR |
| 111585 | cg07297467 | 0.1250 | 0.0296 | 2.42e-05 | +++ | 0.1031703 | 1.0000000 | chr2 | 101635691 | RPL31;TBC1D8 | 3’UTR;Body |
| 317171 | cg22988651 | 0.1333 | 0.0316 | 2.43e-05 | +++ | 0.1031703 | 1.0000000 | chr3 | 15792635 | ANKRD28 | Body |
| 26185 | cg01614020 | 0.2810 | 0.0666 | 2.44e-05 | +++ | 0.1031703 | 1.0000000 | chr8 | 24814137 | NEFL | TSS200 |
| 190817 | cg13208054 | 0.0820 | 0.0194 | 2.47e-05 | +++ | 0.1031703 | 1.0000000 | chr17 | 25936354 | KSR1 | Body |
| 153219 | cg10273420 | -0.0916 | 0.0217 | 2.49e-05 | -+- | 0.1031703 | 1.0000000 | chr10 | 43953760 | ZNF487 | Body |
| 308465 | cg22261158 | 0.1292 | 0.0307 | 2.53e-05 | +++ | 0.1037305 | 1.0000000 | chr12 | 98941654 | TMPO;TMPO | 3’UTR;3’UTR |
| 201631 | cg13909585 | 0.2349 | 0.0559 | 2.61e-05 | +++ | 0.1041717 | 1.0000000 | chr7 | 82792379 | PCLO;PCLO | TSS200;TSS200 |
| 240114 | cg16681246 | 0.0937 | 0.0223 | 2.62e-05 | +++ | 0.1041717 | 1.0000000 | chr2 | 65541310 | SPRED2;SPRED2 | Body;Body |
| 131033 | cg08654960 | -0.1464 | 0.0348 | 2.63e-05 | — | 0.1041717 | 1.0000000 | chr16 | 85319859 | ||
| 31762 | cg01972350 | -0.1407 | 0.0335 | 2.68e-05 | — | 0.1041717 | 1.0000000 | chr17 | 79155695 | LOC388428 | Body |
| 150911 | cg10114235 | 0.1228 | 0.0293 | 2.69e-05 | +++ | 0.1041717 | 1.0000000 | chr6 | 169449059 | ||
| 47856 | cg02996181 | 0.0722 | 0.0172 | 2.71e-05 | ++- | 0.1041717 | 1.0000000 | chr11 | 417643 | SIGIRR;SIGIRR | TSS1500;TSS1500 |
| 199205 | cg13751796 | 0.0845 | 0.0202 | 2.73e-05 | +++ | 0.1041717 | 1.0000000 | chr9 | 132633833 | USP20;USP20;USP20 | Body;Body;Body |
| 229928 | cg15931233 | 0.1027 | 0.0245 | 2.77e-05 | +++ | 0.1046017 | 1.0000000 | chr5 | 53455496 | ARL15 | Body |
| X | ONTOLOGY | TERM | N | DE | P.DE | FDR |
|---|---|---|---|---|---|---|
| GO:0048545 | BP | response to steroid hormone | 329 | 8 | 0.0002538 | 1 |
| GO:2000171 | BP | negative regulation of dendrite development | 25 | 3 | 0.0006726 | 1 |
| GO:0003044 | BP | regulation of systemic arterial blood pressure mediated by a chemical signal | 45 | 3 | 0.0009954 | 1 |
| GO:0070972 | BP | protein localization to endoplasmic reticulum | 134 | 4 | 0.0011312 | 1 |
| GO:0009725 | BP | response to hormone | 863 | 12 | 0.0013203 | 1 |
| GO:0032570 | BP | response to progesterone | 45 | 3 | 0.0015462 | 1 |
| GO:0031307 | CC | integral component of mitochondrial outer membrane | 19 | 2 | 0.0030355 | 1 |
| GO:0099631 | CC | postsynaptic endocytic zone cytoplasmic component | 2 | 1 | 0.0031890 | 1 |
| GO:0031306 | CC | intrinsic component of mitochondrial outer membrane | 20 | 2 | 0.0034739 | 1 |
| GO:0071383 | BP | cellular response to steroid hormone stimulus | 194 | 5 | 0.0035536 | 1 |
| GO:0030728 | BP | ovulation | 20 | 2 | 0.0035557 | 1 |
| GO:0050774 | BP | negative regulation of dendrite morphogenesis | 14 | 2 | 0.0039691 | 1 |
| GO:0006979 | BP | response to oxidative stress | 434 | 7 | 0.0040529 | 1 |
| GO:0061000 | BP | negative regulation of dendritic spine development | 11 | 2 | 0.0041920 | 1 |
| GO:0004990 | MF | oxytocin receptor activity | 1 | 1 | 0.0046387 | 1 |
| GO:0006305 | BP | DNA alkylation | 71 | 3 | 0.0047397 | 1 |
| GO:0006306 | BP | DNA methylation | 71 | 3 | 0.0047397 | 1 |
| GO:0016010 | CC | dystrophin-associated glycoprotein complex | 18 | 2 | 0.0047560 | 1 |
| GO:0090665 | CC | glycoprotein complex | 18 | 2 | 0.0047560 | 1 |
| GO:0061318 | BP | renal filtration cell differentiation | 18 | 2 | 0.0051905 | 1 |
| GO:0072112 | BP | glomerular visceral epithelial cell differentiation | 18 | 2 | 0.0051905 | 1 |
| GO:0050886 | BP | endocrine process | 78 | 3 | 0.0054921 | 1 |
| GO:0010335 | BP | response to non-ionic osmotic stress | 1 | 1 | 0.0056612 | 1 |
| GO:0071471 | BP | cellular response to non-ionic osmotic stress | 1 | 1 | 0.0056612 | 1 |
| GO:0007613 | BP | memory | 116 | 4 | 0.0056747 | 1 |
| GO:1903524 | BP | positive regulation of blood circulation | 72 | 3 | 0.0056822 | 1 |
| GO:0072311 | BP | glomerular epithelial cell differentiation | 19 | 2 | 0.0057171 | 1 |
| GO:0044703 | BP | multi-organism reproductive process | 943 | 10 | 0.0062853 | 1 |
| GO:0072010 | BP | glomerular epithelium development | 22 | 2 | 0.0066983 | 1 |
| GO:0043401 | BP | steroid hormone mediated signaling pathway | 131 | 4 | 0.0067175 | 1 |
| GO:0004666 | MF | prostaglandin-endoperoxide synthase activity | 2 | 1 | 0.0070536 | 1 |
| GO:0090362 | BP | positive regulation of platelet-derived growth factor production | 2 | 1 | 0.0073248 | 1 |
| GO:0034643 | BP | establishment of mitochondrion localization, microtubule-mediated | 22 | 2 | 0.0074343 | 1 |
| GO:0047497 | BP | mitochondrion transport along microtubule | 22 | 2 | 0.0074343 | 1 |
| GO:0030371 | MF | translation repressor activity | 24 | 2 | 0.0079009 | 1 |
| GO:0003073 | BP | regulation of systemic arterial blood pressure | 87 | 3 | 0.0079262 | 1 |
| GO:0051654 | BP | establishment of mitochondrion localization | 25 | 2 | 0.0086020 | 1 |
| GO:0001990 | BP | regulation of systemic arterial blood pressure by hormone | 35 | 2 | 0.0087258 | 1 |
| GO:0007565 | BP | female pregnancy | 175 | 4 | 0.0088200 | 1 |
| GO:0008217 | BP | regulation of blood pressure | 175 | 4 | 0.0088372 | 1 |
| GO:0044728 | BP | DNA methylation or demethylation | 94 | 3 | 0.0091241 | 1 |
| GO:2000815 | BP | regulation of mRNA stability involved in response to oxidative stress | 2 | 1 | 0.0091562 | 1 |
| GO:0030660 | CC | Golgi-associated vesicle membrane | 103 | 3 | 0.0091582 | 1 |
| GO:0035037 | BP | sperm entry | 1 | 1 | 0.0093095 | 1 |
| GO:0061795 | BP | Golgi lumen acidification | 1 | 1 | 0.0093095 | 1 |
| GO:1905526 | BP | regulation of Golgi lumen acidification | 1 | 1 | 0.0093095 | 1 |
| GO:1905528 | BP | positive regulation of Golgi lumen acidification | 1 | 1 | 0.0093095 | 1 |
| GO:0030431 | BP | sleep | 34 | 2 | 0.0098816 | 1 |
| GO:0045987 | BP | positive regulation of smooth muscle contraction | 31 | 2 | 0.0099122 | 1 |
| GO:0031337 | BP | positive regulation of sulfur amino acid metabolic process | 1 | 1 | 0.0099457 | 1 |
| GO:0050668 | BP | positive regulation of homocysteine metabolic process | 1 | 1 | 0.0099457 | 1 |
| GO:0045777 | BP | positive regulation of blood pressure | 37 | 2 | 0.0099634 | 1 |
| GO:0051704 | BP | multi-organism process | 1013 | 10 | 0.0100226 | 1 |
| GO:0003065 | BP | positive regulation of heart rate by epinephrine | 1 | 1 | 0.0103331 | 1 |
| GO:0001992 | BP | regulation of systemic arterial blood pressure by vasopressin | 4 | 1 | 0.0107040 | 1 |
| GO:1905550 | BP | regulation of protein localization to endoplasmic reticulum | 2 | 1 | 0.0108268 | 1 |
| GO:1905552 | BP | positive regulation of protein localization to endoplasmic reticulum | 2 | 1 | 0.0108268 | 1 |
| GO:0005046 | MF | KDEL sequence binding | 3 | 1 | 0.0108284 | 1 |
| GO:0019098 | BP | reproductive behavior | 30 | 2 | 0.0109375 | 1 |
| GO:1905636 | BP | positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding | 3 | 1 | 0.0109386 | 1 |
| GO:0035936 | BP | testosterone secretion | 2 | 1 | 0.0111017 | 1 |
| GO:2000843 | BP | regulation of testosterone secretion | 2 | 1 | 0.0111017 | 1 |
| GO:2000845 | BP | positive regulation of testosterone secretion | 2 | 1 | 0.0111017 | 1 |
| GO:0072299 | BP | negative regulation of metanephric glomerulus development | 1 | 1 | 0.0111036 | 1 |
| GO:0072302 | BP | negative regulation of metanephric glomerular mesangial cell proliferation | 1 | 1 | 0.0111036 | 1 |
| GO:0071284 | BP | cellular response to lead ion | 3 | 1 | 0.0111855 | 1 |
| GO:0035023 | BP | regulation of Rho protein signal transduction | 79 | 3 | 0.0112261 | 1 |
| GO:1903895 | BP | negative regulation of IRE1-mediated unfolded protein response | 5 | 1 | 0.0114765 | 1 |
| GO:0004382 | MF | guanosine-diphosphatase activity | 2 | 1 | 0.0115044 | 1 |
| GO:1902626 | BP | assembly of large subunit precursor of preribosome | 3 | 1 | 0.0115739 | 1 |
| GO:0047191 | MF | 1-alkylglycerophosphocholine O-acyltransferase activity | 1 | 1 | 0.0117615 | 1 |
| GO:2001246 | BP | negative regulation of phosphatidylcholine biosynthetic process | 1 | 1 | 0.0117615 | 1 |
| GO:0003908 | MF | methylated-DNA-[protein]-cysteine S-methyltransferase activity | 1 | 1 | 0.0117914 | 1 |
| GO:0043001 | BP | Golgi to plasma membrane protein transport | 39 | 2 | 0.0120581 | 1 |
| GO:0050666 | BP | regulation of homocysteine metabolic process | 2 | 1 | 0.0125404 | 1 |
| GO:0007612 | BP | learning | 140 | 4 | 0.0126947 | 1 |
| GO:0014070 | BP | response to organic cyclic compound | 885 | 10 | 0.0129020 | 1 |
| GO:0032870 | BP | cellular response to hormone stimulus | 602 | 8 | 0.0133645 | 1 |
| GO:0045907 | BP | positive regulation of vasoconstriction | 33 | 2 | 0.0134807 | 1 |
| GO:0006304 | BP | DNA modification | 116 | 3 | 0.0138524 | 1 |
| GO:1990564 | BP | protein polyufmylation | 5 | 1 | 0.0138602 | 1 |
| GO:1990592 | BP | protein K69-linked ufmylation | 5 | 1 | 0.0138602 | 1 |
| GO:0090360 | BP | platelet-derived growth factor production | 3 | 1 | 0.0139227 | 1 |
| GO:0090361 | BP | regulation of platelet-derived growth factor production | 3 | 1 | 0.0139227 | 1 |
| GO:0008585 | BP | female gonad development | 96 | 3 | 0.0140875 | 1 |
| GO:0047159 | MF | 1-alkenylglycerophosphocholine O-acyltransferase activity | 2 | 1 | 0.0144966 | 1 |
| GO:0050200 | MF | plasmalogen synthase activity | 2 | 1 | 0.0144966 | 1 |
| GO:0044706 | BP | multi-multicellular organism process | 204 | 4 | 0.0146238 | 1 |
| GO:0001544 | BP | initiation of primordial ovarian follicle growth | 2 | 1 | 0.0151198 | 1 |
| GO:0005150 | MF | interleukin-1, type I receptor binding | 2 | 1 | 0.0152167 | 1 |
| GO:0072301 | BP | regulation of metanephric glomerular mesangial cell proliferation | 2 | 1 | 0.0155594 | 1 |
| GO:1900169 | BP | regulation of glucocorticoid mediated signaling pathway | 2 | 1 | 0.0155805 | 1 |
| GO:0047192 | MF | 1-alkylglycerophosphocholine O-acetyltransferase activity | 3 | 1 | 0.0156545 | 1 |
| GO:0071963 | BP | establishment or maintenance of cell polarity regulating cell shape | 2 | 1 | 0.0158844 | 1 |
| GO:0045764 | BP | positive regulation of cellular amino acid metabolic process | 3 | 1 | 0.0162795 | 1 |
| GO:0016206 | MF | catechol O-methyltransferase activity | 2 | 1 | 0.0163029 | 1 |
| GO:0102084 | MF | L-dopa O-methyltransferase activity | 2 | 1 | 0.0163029 | 1 |
| GO:0102938 | MF | orcinol O-methyltransferase activity | 2 | 1 | 0.0163029 | 1 |
| GO:0046545 | BP | development of primary female sexual characteristics | 100 | 3 | 0.0163060 | 1 |
| GO:0034059 | BP | response to anoxia | 3 | 1 | 0.0164205 | 1 |
metal_all_cell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/all_cell_common_DVP_1204201.tbl', sep = "\t")
metal_all_cell_DVP = metalProcess(metal_all_cell_DVP)
write.csv(metal_all_cell_DVP, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DVP_all_cell_common_120420.csv')
# Significant probes
# Nominal P-value
table(metal_all_cell_DVP$P.value < 0.05)
# FALSE TRUE
# 348952 28399
# FDR
table(metal_all_cell_DVP$P.FDR < 0.05)
# FALSE TRUE
# 377332 19
table(metal_all_cell_DVP$P.FDR < 0.1)
# FALSE TRUE
# 377245 106
# Bonferroni
table(metal_all_cell_DVP$P.Bonf < 0.05)
# FALSE TRUE
# 377346 5
# GO analysis, FDR < 0.1 probes
go_metal_all_cell_DVP = gometh(sig.cpg = metal_all_cell_DVP$Name[metal_all_cell_DVP$P.FDR < 0.1], all.cpg = metal_all_cell_DVP$Name, array.type = '450K', anno = annAll2)
go_metal_all_cell_DVP = go_metal_all_cell_DVP[order(go_metal_all_cell_DVP$P.DE),]
table(go_metal_all_cell_DVP$P.DE<0.05)
# FALSE TRUE
# 22314 269
table(go_metal_all_cell_DVP$FDR<0.05)
# FALSE
# 22583
write.csv(go_metal_all_cell_DVP[go_metal_all_cell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DVP_all_cell_common_120420.csv')
# KEGG analysis, FDR < 0.1 probes
kegg_metal_all_cell_DVP = gometh(sig.cpg = metal_all_cell_DVP$Name[metal_all_cell_DVP$P.FDR < 0.1], all.cpg = metal_all_cell_DVP$Name, array.type = '450K', collection = 'KEGG', sig.genes = T, anno = annAll2)
kegg_metal_all_cell_DVP = kegg_metal_all_cell_DVP[order(kegg_metal_all_cell_DVP$P.DE),]
table(kegg_metal_all_cell_DVP$P.DE<0.05)
# FALSE TRUE
# 336 4
table(kegg_metal_all_cell_DVP$FDR<0.05)
# FALSE
# 340
write.csv(kegg_metal_all_cell_DVP[kegg_metal_all_cell_DVP$P.DE < 0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DVP_all_cell_common_120420.csv')
# Plotting
gg_qqplot(metal_all_cell_DVP$P.value)
quartz.save('qq_metal_all_cell_DVP_120420.png', type = "png", dpi = 300)
manhattan_meta(metal_all_cell_DVP, FDR=T)
quartz.save('manhattan_metal_all_cell_DVP_120420.png', type = "png", dpi = 300)
volcano_meta(metal_all_cell_DVP, FDR = TRUE)
quartz.save('volcano_metal_all_cell_DVP_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_all_cell_DVP_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_all_cell_DVP_120420.png")
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_all_cell_DVP_120420.png")
| X | Name | Effect | StdErr | P.value | Direction | P.FDR | P.Bonf | chr | pos | UCSC_RefGene_Name | UCSC_RefGene_Group |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 321132 | cg23281729 | 0.9945 | 0.1300 | 0.00e+00 | -+++ | 0.0000000 | 0.0000000 | chr18 | 78005477 | PARD6G | TSS200 |
| 374163 | cg27425262 | 0.8952 | 0.1237 | 0.00e+00 | ++++ | 0.0000001 | 0.0000002 | chr2 | 113953981 | PSD4;LOC440839 | Body;Body |
| 50934 | cg03205258 | 0.6446 | 0.1117 | 0.00e+00 | ++++ | 0.0010001 | 0.0030003 | chr22 | 19929274 | TXNRD2;COMT;COMT | 1stExon;1stExon;5’UTR |
| 163279 | cg11032634 | 0.6967 | 0.1285 | 1.00e-07 | ++++ | 0.0056225 | 0.0224901 | chr22 | 19929254 | TXNRD2;COMT | 1stExon;TSS200 |
| 64158 | cg04080724 | 0.1394 | 0.0263 | 1.00e-07 | ++++ | 0.0085810 | 0.0429048 | chr4 | 140202327 | C4orf49 | TSS1500 |
| 360213 | cg26384602 | -0.1222 | 0.0234 | 2.00e-07 | —- | 0.0102424 | 0.0705646 | chr19 | 41798386 | HNRNPUL1;HNRNPUL1 | Body;Body |
| 167567 | cg11361658 | 0.1562 | 0.0300 | 2.00e-07 | ++++ | 0.0102424 | 0.0716967 | chr5 | 128452311 | ||
| 145256 | cg09692492 | -0.2979 | 0.0576 | 2.00e-07 | —- | 0.0109290 | 0.0874322 | chr22 | 23744717 | ZDHHC8P | Body |
| 314099 | cg22749736 | 0.1176 | 0.0232 | 4.00e-07 | ++++ | 0.0175929 | 0.1583365 | chr11 | 1306759 | TOLLIP | Body |
| 304645 | cg21921619 | -0.1465 | 0.0292 | 5.00e-07 | -+– | 0.0206675 | 0.2066751 | chr10 | 116852791 | ATRNL1 | TSS1500 |
| 120767 | cg07935287 | -0.1330 | 0.0269 | 8.00e-07 | —- | 0.0257416 | 0.2984469 | chr18 | 54318347 | WDR7;WDR7 | TSS1500;TSS1500 |
| 80568 | cg05169951 | 0.2169 | 0.0440 | 8.00e-07 | ++++ | 0.0257416 | 0.3088995 | chr16 | 3017955 | KREMEN2;PAQR4;KREMEN2 | Body;TSS1500;Body |
| 295936 | cg21185289 | 0.3705 | 0.0758 | 1.00e-06 | ++++ | 0.0293463 | 0.3815019 | chr2 | 74743437 | TLX2 | 3’UTR |
| 309909 | cg22387890 | 0.4772 | 0.0980 | 1.10e-06 | ++++ | 0.0302689 | 0.4237652 | chr7 | 6145595 | USP42 | 5’UTR |
| 190387 | cg13171197 | 0.1174 | 0.0244 | 1.50e-06 | +-++ | 0.0366266 | 0.5524419 | chr7 | 90916020 | ||
| 339841 | cg24754507 | -0.1026 | 0.0214 | 1.60e-06 | —- | 0.0366266 | 0.5860261 | chr6 | 28481862 | GPX6 | Body |
| 5963 | cg00355447 | 0.1410 | 0.0295 | 1.80e-06 | ++++ | 0.0392864 | 0.6792318 | chr6 | 30292220 | HCG18;HCG18 | Body;Body |
| 237588 | cg16511076 | 0.1215 | 0.0255 | 1.90e-06 | +++- | 0.0392864 | 0.7071558 | chr4 | 48887480 | OCIAD2;OCIAD2 | 3’UTR;3’UTR |
| 76120 | cg04873963 | -0.1029 | 0.0218 | 2.50e-06 | —- | 0.0487577 | 0.9263967 | chr16 | 2518322 | ||
| 124685 | cg08207566 | 0.1154 | 0.0246 | 2.80e-06 | +++- | 0.0533763 | 1.0000000 | chr4 | 174086461 | ||
| 102811 | cg06740986 | 0.0989 | 0.0213 | 3.30e-06 | ++++ | 0.0588488 | 1.0000000 | chr1 | 184838417 | FAM129A | Body |
| 167176 | cg11332363 | 0.2113 | 0.0456 | 3.50e-06 | ++++ | 0.0598616 | 1.0000000 | chr19 | 54023999 | ZNF331 | TSS200 |
| 302848 | cg21774561 | 0.1147 | 0.0248 | 3.70e-06 | ++++ | 0.0604862 | 1.0000000 | chr17 | 80209247 | CSNK1D;CSNK1D | Body;Body |
| 219690 | cg15104380 | -0.0861 | 0.0186 | 3.80e-06 | +— | 0.0604862 | 1.0000000 | chr10 | 99285205 | UBTD1 | Body |
| 303849 | cg21857098 | 0.1019 | 0.0222 | 4.60e-06 | ++++ | 0.0647340 | 1.0000000 | chr15 | 25638137 | UBE3A;UBE3A;UBE3A | Body;Body;Body |
| 293675 | cg21004290 | 0.1266 | 0.0277 | 4.80e-06 | ++++ | 0.0647340 | 1.0000000 | chr8 | 131250320 | ASAP1 | Body |
| 193559 | cg13411311 | -0.1008 | 0.0220 | 4.80e-06 | —- | 0.0647340 | 1.0000000 | chr2 | 241095989 | ||
| 161566 | cg10898607 | -0.1144 | 0.0250 | 4.80e-06 | —- | 0.0647340 | 1.0000000 | chr3 | 101405733 | RPL24 | TSS200 |
| 129911 | cg08575722 | -0.1427 | 0.0313 | 5.10e-06 | —- | 0.0647340 | 1.0000000 | chr11 | 32421845 | WT1;WT1;WT1;WT1 | Body;Body;Body;Body |
| 189046 | cg13054212 | 0.0959 | 0.0211 | 5.30e-06 | ++++ | 0.0647340 | 1.0000000 | chr4 | 186356202 | C4orf47 | Body |
| 214646 | cg14718822 | -0.1498 | 0.0329 | 5.30e-06 | -+– | 0.0647340 | 1.0000000 | chr6 | 84234250 | PRSS35;PRSS35 | Body;Body |
| 28677 | cg01783101 | 0.2343 | 0.0517 | 5.80e-06 | ++++ | 0.0653810 | 1.0000000 | chr7 | 118498931 | ||
| 334867 | cg24376022 | 0.1055 | 0.0233 | 6.10e-06 | ++++ | 0.0653810 | 1.0000000 | chr2 | 3215598 | TSSC1 | Body |
| 11047 | cg00657529 | 0.0940 | 0.0208 | 6.30e-06 | ++++ | 0.0653810 | 1.0000000 | chr6 | 31698687 | CLIC1;DDAH2 | Body;TSS1500 |
| 191734 | cg13281248 | 0.1068 | 0.0237 | 6.50e-06 | ++++ | 0.0653810 | 1.0000000 | chr4 | 1244360 | C4orf42;CTBP1;CTBP1;C4orf42 | 5’UTR;TSS1500;TSS1500;1stExon |
| 179110 | cg12235073 | 0.1203 | 0.0267 | 6.50e-06 | ++-+ | 0.0653810 | 1.0000000 | chr10 | 6270423 | PFKFB3;PFKFB3 | Body;Body |
| 243979 | cg16991858 | 0.0921 | 0.0204 | 6.60e-06 | ++++ | 0.0653810 | 1.0000000 | chr1 | 244612113 | ADSS | Body |
| 337569 | cg24587312 | -0.0682 | 0.0151 | 6.60e-06 | ++– | 0.0653810 | 1.0000000 | chr15 | 39766341 | ||
| 282709 | cg20066496 | -0.1849 | 0.0411 | 6.80e-06 | +— | 0.0654478 | 1.0000000 | chr15 | 43213993 | TTBK2 | TSS1500 |
| 271236 | cg19170881 | -0.1914 | 0.0427 | 7.30e-06 | —- | 0.0654478 | 1.0000000 | chr7 | 101129980 | EMID2 | Body |
| 150964 | cg10117884 | 0.1224 | 0.0273 | 7.40e-06 | ++++ | 0.0654478 | 1.0000000 | chr1 | 166955898 | ||
| 162593 | cg10980774 | 0.1646 | 0.0368 | 7.50e-06 | ++++ | 0.0654478 | 1.0000000 | chr11 | 112832547 | NCAM1;NCAM1;NCAM1 | Body;Body;Body |
| 119872 | cg07875335 | 0.2405 | 0.0537 | 7.60e-06 | ++++ | 0.0654478 | 1.0000000 | chr2 | 48844728 | GTF2A1L;GTF2A1L;STON1-GTF2A1L | TSS1500;TSS1500;Body |
| 126025 | cg08293531 | -0.0993 | 0.0222 | 7.80e-06 | —- | 0.0654478 | 1.0000000 | chr15 | 101601180 | LRRK1 | Body |
| 140791 | cg09366379 | -0.2971 | 0.0666 | 8.20e-06 | —- | 0.0654478 | 1.0000000 | chr16 | 87905824 | ||
| 116190 | cg07611790 | 0.0956 | 0.0215 | 8.40e-06 | +++- | 0.0654478 | 1.0000000 | chr19 | 49240823 | RASIP1 | Body |
| 292637 | cg20923605 | 0.3039 | 0.0682 | 8.40e-06 | ++++ | 0.0654478 | 1.0000000 | chr13 | 112978683 | ||
| 188976 | cg13049359 | 0.1933 | 0.0434 | 8.50e-06 | +-++ | 0.0654478 | 1.0000000 | chr4 | 188891490 | ||
| 159378 | cg10729167 | 0.1545 | 0.0347 | 8.60e-06 | ++++ | 0.0654478 | 1.0000000 | chr10 | 111220101 | ||
| 23625 | cg01445793 | 0.1912 | 0.0430 | 8.70e-06 | ++++ | 0.0654478 | 1.0000000 | chr17 | 3771578 | CAMKK1;CAMKK1;CAMKK1 | Body;Body;Body |
| 265593 | cg18703721 | 0.1163 | 0.0262 | 9.40e-06 | ++++ | 0.0660776 | 1.0000000 | chr10 | 75282672 | USP54 | Body |
| 202666 | cg13972353 | 0.1266 | 0.0286 | 9.50e-06 | +++- | 0.0660776 | 1.0000000 | chr9 | 139354348 | SEC16A | Body |
| 178342 | cg12175949 | 0.3017 | 0.0682 | 9.60e-06 | ++++ | 0.0660776 | 1.0000000 | chr22 | 19929286 | TXNRD2;COMT;COMT | 1stExon;1stExon;5’UTR |
| 148318 | cg09920145 | -0.0958 | 0.0216 | 9.60e-06 | —- | 0.0660776 | 1.0000000 | chr3 | 69100714 | TMF1 | Body |
| 125889 | cg08285768 | 0.1000 | 0.0226 | 9.60e-06 | +++- | 0.0660776 | 1.0000000 | chr15 | 86038622 | AKAP13;AKAP13 | Body;Body |
| 144882 | cg09664373 | 0.1149 | 0.0260 | 1.01e-05 | ++++ | 0.0661963 | 1.0000000 | chr16 | 968219 | LMF1 | Body |
| 232066 | cg16101346 | 0.1496 | 0.0339 | 1.03e-05 | -+++ | 0.0661963 | 1.0000000 | chr1 | 186650479 | PTGS2 | TSS1500 |
| 300598 | cg21575923 | -0.1390 | 0.0315 | 1.03e-05 | —- | 0.0661963 | 1.0000000 | chr6 | 41139345 | ||
| 110491 | cg07219314 | -0.1723 | 0.0391 | 1.03e-05 | —- | 0.0661963 | 1.0000000 | chr22 | 23744725 | ZDHHC8P | Body |
| 18378 | cg01105932 | 0.1049 | 0.0239 | 1.17e-05 | ++++ | 0.0723453 | 1.0000000 | chr5 | 158635248 | RNF145 | TSS1500 |
| 156000 | cg10485752 | 0.1432 | 0.0327 | 1.20e-05 | ++++ | 0.0723453 | 1.0000000 | chr1 | 26021655 | MAN1C1 | Body |
| 11224 | cg00668103 | 0.1210 | 0.0277 | 1.22e-05 | +++- | 0.0723453 | 1.0000000 | chr7 | 100084730 | C7orf51 | Body |
| 37478 | cg02339198 | 0.1076 | 0.0246 | 1.22e-05 | ++++ | 0.0723453 | 1.0000000 | chr19 | 52693970 | PPP2R1A | Body |
| 33262 | cg02067580 | -0.0638 | 0.0146 | 1.23e-05 | +— | 0.0723453 | 1.0000000 | chr1 | 153606662 | C1orf77;S100A13;C1orf77 | 5’UTR;TSS200;1stExon |
| 280471 | cg19891452 | 0.2885 | 0.0660 | 1.25e-05 | ++++ | 0.0725094 | 1.0000000 | chr13 | 112978703 | ||
| 235393 | cg16353272 | 0.0961 | 0.0221 | 1.35e-05 | ++++ | 0.0736778 | 1.0000000 | chr16 | 2124240 | TSC2;TSC2;TSC2 | Body;Body;Body |
| 114654 | cg07510163 | 0.1519 | 0.0349 | 1.36e-05 | ++++ | 0.0736778 | 1.0000000 | chr2 | 44547313 | PREPL;PREPL;PREPL;PREPL;PREPL;PREPL;SLC3A1;PREPL | 3’UTR;3’UTR;3’UTR;3’UTR;3’UTR;3’UTR;Body;3’UTR |
| 32578 | cg02026246 | 0.1296 | 0.0299 | 1.44e-05 | ++++ | 0.0736778 | 1.0000000 | chr11 | 22687589 | GAS2 | TSS1500 |
| 370643 | cg27155653 | -0.1019 | 0.0235 | 1.44e-05 | —- | 0.0736778 | 1.0000000 | chr1 | 183604774 | ARPC5;RGL1 | 1stExon;TSS1500 |
| 64658 | cg04111999 | 0.1023 | 0.0236 | 1.46e-05 | ++++ | 0.0736778 | 1.0000000 | chr10 | 22615540 | BMI1 | Body |
| 131033 | cg08654960 | -0.1495 | 0.0345 | 1.46e-05 | —- | 0.0736778 | 1.0000000 | chr16 | 85319859 | ||
| 109701 | cg07168204 | 0.1217 | 0.0281 | 1.46e-05 | +++- | 0.0736778 | 1.0000000 | chr5 | 149864599 | ||
| 280816 | cg19916330 | 0.1027 | 0.0237 | 1.47e-05 | ++++ | 0.0736778 | 1.0000000 | chr14 | 68038877 | PLEKHH1 | Body |
| 259615 | cg18228116 | 0.3476 | 0.0803 | 1.49e-05 | -+++ | 0.0736778 | 1.0000000 | chr10 | 133995345 | JAKMIP3 | 3’UTR |
| 98154 | cg06421138 | 0.1083 | 0.0250 | 1.51e-05 | ++++ | 0.0736778 | 1.0000000 | chr6 | 111750934 | REV3L | Body |
| 238518 | cg16573251 | 0.0700 | 0.0162 | 1.53e-05 | ++++ | 0.0736778 | 1.0000000 | chr12 | 123381231 | VPS37B | TSS1500 |
| 339775 | cg24748746 | -0.2174 | 0.0503 | 1.53e-05 | —- | 0.0736778 | 1.0000000 | chr7 | 155738916 | ||
| 291461 | cg20805880 | 0.1014 | 0.0234 | 1.53e-05 | ++++ | 0.0736778 | 1.0000000 | chr15 | 73367293 | NEO1 | Body |
| 121453 | cg07984508 | 0.0906 | 0.0210 | 1.56e-05 | +++- | 0.0736778 | 1.0000000 | chr15 | 77426719 | SGK269 | Body |
| 112621 | cg07367760 | 0.1087 | 0.0252 | 1.56e-05 | ++++ | 0.0736778 | 1.0000000 | chr16 | 2911707 | ||
| 147224 | cg09845489 | 0.2497 | 0.0579 | 1.63e-05 | ++++ | 0.0749701 | 1.0000000 | chr7 | 157667853 | PTPRN2;PTPRN2;PTPRN2 | Body;Body;Body |
| 146726 | cg09809672 | -0.1376 | 0.0319 | 1.64e-05 | —- | 0.0749701 | 1.0000000 | chr1 | 236557682 | EDARADD;EDARADD;EDARADD | TSS1500;5’UTR;1stExon |
| 316511 | cg22938135 | 0.0935 | 0.0217 | 1.65e-05 | +++- | 0.0749701 | 1.0000000 | chr5 | 175841493 | CLTB;CLTB | Body;Body |
| 100415 | cg06581201 | 0.1743 | 0.0405 | 1.67e-05 | ++++ | 0.0749760 | 1.0000000 | chr6 | 168534038 | ||
| 93087 | cg06039392 | 0.1302 | 0.0303 | 1.70e-05 | ++++ | 0.0754702 | 1.0000000 | chr4 | 187476953 | MTNR1A | TSS1500 |
| 343712 | cg25052374 | 0.0771 | 0.0180 | 1.78e-05 | ++++ | 0.0777924 | 1.0000000 | chr17 | 76991253 | CANT1;CANT1;CANT1 | Body;Body;Body |
| 307323 | cg22159421 | -0.3143 | 0.0733 | 1.82e-05 | —- | 0.0777924 | 1.0000000 | chr11 | 34460182 | CAT | TSS1500 |
| 190817 | cg13208054 | 0.0753 | 0.0176 | 1.83e-05 | ++++ | 0.0777924 | 1.0000000 | chr17 | 25936354 | KSR1 | Body |
| 58507 | cg03700279 | 0.1001 | 0.0234 | 1.86e-05 | +++- | 0.0777924 | 1.0000000 | chr2 | 44576358 | PREPL;PREPL;PREPL;PREPL;PREPL;PREPL;PREPL | Body;Body;5’UTR;5’UTR;Body;Body;Body |
| 156274 | cg10502904 | 0.1460 | 0.0341 | 1.87e-05 | ++++ | 0.0777924 | 1.0000000 | chr10 | 131565289 | MGMT | 3’UTR |
| 301085 | cg21613693 | -0.1303 | 0.0304 | 1.88e-05 | —- | 0.0777924 | 1.0000000 | chr17 | 73501181 | CASKIN2;CASKIN2 | Body;Body |
| 227727 | cg15754901 | 0.1049 | 0.0246 | 1.99e-05 | +-++ | 0.0816637 | 1.0000000 | chr17 | 5402972 | LOC728392 | 3’UTR |
| 336897 | cg24531494 | 0.1549 | 0.0365 | 2.15e-05 | ++++ | 0.0871965 | 1.0000000 | chr4 | 121993049 | C4orf31 | 5’UTR |
| 69534 | cg04426031 | 0.1100 | 0.0260 | 2.27e-05 | ++++ | 0.0905245 | 1.0000000 | chr7 | 1799192 | ||
| 114218 | cg07479711 | 0.1114 | 0.0263 | 2.28e-05 | ++++ | 0.0905245 | 1.0000000 | chr5 | 1524940 | LPCAT1 | TSS1500 |
| 248409 | cg17332762 | 0.0966 | 0.0228 | 2.31e-05 | +++- | 0.0906822 | 1.0000000 | chr3 | 106967639 | LOC344595;LOC344595 | Body;Body |
| 35145 | cg02192228 | 0.1758 | 0.0416 | 2.38e-05 | ++++ | 0.0921815 | 1.0000000 | chr3 | 8809536 | OXTR | Body |
| 171628 | cg11691429 | 0.1703 | 0.0403 | 2.39e-05 | +++- | 0.0921815 | 1.0000000 | chr2 | 947634 | SNTG2 | Body |
| 128672 | cg08487455 | 0.1666 | 0.0395 | 2.46e-05 | ++++ | 0.0936517 | 1.0000000 | chr16 | 76311050 | CNTNAP4 | TSS200 |
| 202290 | cg13946520 | 0.2956 | 0.0701 | 2.48e-05 | -+++ | 0.0936585 | 1.0000000 | chr2 | 87017689 | CD8A;CD8A;CD8A;CD8A | Body;Body;Body;Body |
| X | ONTOLOGY | TERM | N | DE | P.DE | FDR |
|---|---|---|---|---|---|---|
| GO:0016209 | MF | antioxidant activity | 83 | 4 | 0.0003353 | 1 |
| GO:0098869 | BP | cellular oxidant detoxification | 97 | 4 | 0.0008096 | 1 |
| GO:0004601 | MF | peroxidase activity | 49 | 3 | 0.0009488 | 1 |
| GO:1990748 | BP | cellular detoxification | 107 | 4 | 0.0010205 | 1 |
| GO:2000171 | BP | negative regulation of dendrite development | 25 | 3 | 0.0010763 | 1 |
| GO:0016684 | MF | oxidoreductase activity, acting on peroxide as acceptor | 53 | 3 | 0.0012599 | 1 |
| GO:0097237 | BP | cellular response to toxic substance | 114 | 4 | 0.0016410 | 1 |
| GO:0098754 | BP | detoxification | 130 | 4 | 0.0016700 | 1 |
| GO:0005794 | CC | Golgi apparatus | 1477 | 17 | 0.0030512 | 1 |
| GO:0099631 | CC | postsynaptic endocytic zone cytoplasmic component | 2 | 1 | 0.0031425 | 1 |
| GO:0005078 | MF | MAP-kinase scaffold activity | 11 | 2 | 0.0036667 | 1 |
| GO:0030728 | BP | ovulation | 20 | 2 | 0.0043379 | 1 |
| GO:0051232 | BP | meiotic spindle elongation | 1 | 1 | 0.0047115 | 1 |
| GO:0004990 | MF | oxytocin receptor activity | 1 | 1 | 0.0049495 | 1 |
| GO:0050774 | BP | negative regulation of dendrite morphogenesis | 14 | 2 | 0.0052437 | 1 |
| GO:0032225 | BP | regulation of synaptic transmission, dopaminergic | 16 | 2 | 0.0053970 | 1 |
| GO:0010335 | BP | response to non-ionic osmotic stress | 1 | 1 | 0.0059936 | 1 |
| GO:0071471 | BP | cellular response to non-ionic osmotic stress | 1 | 1 | 0.0059936 | 1 |
| GO:0061000 | BP | negative regulation of dendritic spine development | 11 | 2 | 0.0060264 | 1 |
| GO:0010288 | BP | response to lead ion | 22 | 2 | 0.0067367 | 1 |
| GO:0004666 | MF | prostaglandin-endoperoxide synthase activity | 2 | 1 | 0.0073230 | 1 |
| GO:0090362 | BP | positive regulation of platelet-derived growth factor production | 2 | 1 | 0.0075212 | 1 |
| GO:0050886 | BP | endocrine process | 78 | 3 | 0.0076888 | 1 |
| GO:0051704 | BP | multi-organism process | 1013 | 11 | 0.0080764 | 1 |
| GO:0097711 | BP | ciliary basal body-plasma membrane docking | 91 | 3 | 0.0103511 | 1 |
| GO:0001990 | BP | regulation of systemic arterial blood pressure by hormone | 35 | 2 | 0.0105805 | 1 |
| GO:0001992 | BP | regulation of systemic arterial blood pressure by vasopressin | 4 | 1 | 0.0106572 | 1 |
| GO:0035037 | BP | sperm entry | 1 | 1 | 0.0108844 | 1 |
| GO:0061795 | BP | Golgi lumen acidification | 1 | 1 | 0.0108844 | 1 |
| GO:1905526 | BP | regulation of Golgi lumen acidification | 1 | 1 | 0.0108844 | 1 |
| GO:1905528 | BP | positive regulation of Golgi lumen acidification | 1 | 1 | 0.0108844 | 1 |
| GO:1903537 | BP | meiotic cell cycle process involved in oocyte maturation | 2 | 1 | 0.0112336 | 1 |
| GO:1903538 | BP | regulation of meiotic cell cycle process involved in oocyte maturation | 2 | 1 | 0.0112336 | 1 |
| GO:0048545 | BP | response to steroid hormone | 329 | 6 | 0.0116089 | 1 |
| GO:0019953 | BP | sexual reproduction | 791 | 9 | 0.0117434 | 1 |
| GO:0050321 | MF | tau-protein kinase activity | 22 | 2 | 0.0117656 | 1 |
| GO:0031337 | BP | positive regulation of sulfur amino acid metabolic process | 1 | 1 | 0.0119192 | 1 |
| GO:0050668 | BP | positive regulation of homocysteine metabolic process | 1 | 1 | 0.0119192 | 1 |
| GO:0071284 | BP | cellular response to lead ion | 3 | 1 | 0.0120588 | 1 |
| GO:0045987 | BP | positive regulation of smooth muscle contraction | 31 | 2 | 0.0121754 | 1 |
| GO:1902626 | BP | assembly of large subunit precursor of preribosome | 3 | 1 | 0.0122891 | 1 |
| GO:0048609 | BP | multicellular organismal reproductive process | 769 | 9 | 0.0124007 | 1 |
| GO:0035936 | BP | testosterone secretion | 2 | 1 | 0.0124744 | 1 |
| GO:2000843 | BP | regulation of testosterone secretion | 2 | 1 | 0.0124744 | 1 |
| GO:2000845 | BP | positive regulation of testosterone secretion | 2 | 1 | 0.0124744 | 1 |
| GO:0004382 | MF | guanosine-diphosphatase activity | 2 | 1 | 0.0132654 | 1 |
| GO:0032504 | BP | multicellular organism reproduction | 789 | 9 | 0.0133388 | 1 |
| GO:0044703 | BP | multi-organism reproductive process | 943 | 10 | 0.0136047 | 1 |
| GO:0072299 | BP | negative regulation of metanephric glomerulus development | 1 | 1 | 0.0140367 | 1 |
| GO:0072302 | BP | negative regulation of metanephric glomerular mesangial cell proliferation | 1 | 1 | 0.0140367 | 1 |
| GO:0019098 | BP | reproductive behavior | 30 | 2 | 0.0140944 | 1 |
| GO:0050666 | BP | regulation of homocysteine metabolic process | 2 | 1 | 0.0143875 | 1 |
| GO:0004046 | MF | aminoacylase activity | 5 | 1 | 0.0145101 | 1 |
| GO:1904527 | BP | negative regulation of microtubule binding | 2 | 1 | 0.0147022 | 1 |
| GO:0043001 | BP | Golgi to plasma membrane protein transport | 39 | 2 | 0.0147435 | 1 |
| GO:0090360 | BP | platelet-derived growth factor production | 3 | 1 | 0.0148222 | 1 |
| GO:0090361 | BP | regulation of platelet-derived growth factor production | 3 | 1 | 0.0148222 | 1 |
| GO:0008446 | MF | GDP-mannose 4,6-dehydratase activity | 1 | 1 | 0.0148750 | 1 |
| GO:0047191 | MF | 1-alkylglycerophosphocholine O-acyltransferase activity | 1 | 1 | 0.0152431 | 1 |
| GO:2001246 | BP | negative regulation of phosphatidylcholine biosynthetic process | 1 | 1 | 0.0152431 | 1 |
| GO:0003908 | MF | methylated-DNA-[protein]-cysteine S-methyltransferase activity | 1 | 1 | 0.0152953 | 1 |
| GO:0001963 | BP | synaptic transmission, dopaminergic | 27 | 2 | 0.0157612 | 1 |
| GO:0010193 | BP | response to ozone | 4 | 1 | 0.0157812 | 1 |
| GO:0004019 | MF | adenylosuccinate synthase activity | 2 | 1 | 0.0158240 | 1 |
| GO:1902816 | BP | regulation of protein localization to microtubule | 5 | 1 | 0.0166441 | 1 |
| GO:1902817 | BP | negative regulation of protein localization to microtubule | 5 | 1 | 0.0166441 | 1 |
| GO:0045907 | BP | positive regulation of vasoconstriction | 33 | 2 | 0.0167987 | 1 |
| GO:0033596 | CC | TSC1-TSC2 complex | 2 | 1 | 0.0169103 | 1 |
| GO:0051754 | BP | meiotic sister chromatid cohesion, centromeric | 4 | 1 | 0.0170654 | 1 |
| GO:0001544 | BP | initiation of primordial ovarian follicle growth | 2 | 1 | 0.0173561 | 1 |
| GO:0014065 | BP | phosphatidylinositol 3-kinase signaling | 152 | 4 | 0.0174938 | 1 |
| GO:0047159 | MF | 1-alkenylglycerophosphocholine O-acyltransferase activity | 2 | 1 | 0.0179564 | 1 |
| GO:0050200 | MF | plasmalogen synthase activity | 2 | 1 | 0.0179564 | 1 |
| GO:0021935 | BP | cerebellar granule cell precursor tangential migration | 2 | 1 | 0.0180708 | 1 |
| GO:0008502 | MF | melatonin receptor activity | 3 | 1 | 0.0182369 | 1 |
| GO:0033365 | BP | protein localization to organelle | 927 | 10 | 0.0183281 | 1 |
| GO:0034059 | BP | response to anoxia | 3 | 1 | 0.0183810 | 1 |
| GO:0045764 | BP | positive regulation of cellular amino acid metabolic process | 3 | 1 | 0.0185377 | 1 |
| GO:0072301 | BP | regulation of metanephric glomerular mesangial cell proliferation | 2 | 1 | 0.0188547 | 1 |
| GO:0016206 | MF | catechol O-methyltransferase activity | 2 | 1 | 0.0188997 | 1 |
| GO:0102084 | MF | L-dopa O-methyltransferase activity | 2 | 1 | 0.0188997 | 1 |
| GO:0102938 | MF | orcinol O-methyltransferase activity | 2 | 1 | 0.0188997 | 1 |
| GO:1900169 | BP | regulation of glucocorticoid mediated signaling pathway | 2 | 1 | 0.0189176 | 1 |
| GO:0010701 | BP | positive regulation of norepinephrine secretion | 4 | 1 | 0.0190142 | 1 |
| GO:0042713 | BP | sperm ejaculation | 5 | 1 | 0.0191454 | 1 |
| GO:0047192 | MF | 1-alkylglycerophosphocholine O-acetyltransferase activity | 3 | 1 | 0.0191847 | 1 |
| GO:0005150 | MF | interleukin-1, type I receptor binding | 2 | 1 | 0.0192514 | 1 |
| GO:0023024 | MF | MHC class I protein complex binding | 5 | 1 | 0.0193178 | 1 |
| GO:0032227 | BP | negative regulation of synaptic transmission, dopaminergic | 3 | 1 | 0.0193314 | 1 |
| GO:0016036 | BP | cellular response to phosphate starvation | 2 | 1 | 0.0193647 | 1 |
| GO:0043262 | MF | adenosine-diphosphatase activity | 2 | 1 | 0.0194854 | 1 |
| GO:0031335 | BP | regulation of sulfur amino acid metabolic process | 3 | 1 | 0.0195627 | 1 |
| GO:0042351 | BP | ‘de novo’ GDP-L-fucose biosynthetic process | 2 | 1 | 0.0195690 | 1 |
| GO:0008585 | BP | female gonad development | 96 | 3 | 0.0201038 | 1 |
| GO:0031394 | BP | positive regulation of prostaglandin biosynthetic process | 7 | 1 | 0.0202188 | 1 |
| GO:0060359 | BP | response to ammonium ion | 4 | 1 | 0.0202812 | 1 |
| GO:1905424 | BP | regulation of Wnt-mediated midbrain dopaminergic neuron differentiation | 2 | 1 | 0.0203327 | 1 |
| GO:1905426 | BP | positive regulation of Wnt-mediated midbrain dopaminergic neuron differentiation | 2 | 1 | 0.0203327 | 1 |
| GO:0044208 | BP | ‘de novo’ AMP biosynthetic process | 3 | 1 | 0.0203449 | 1 |
| GO:0003044 | BP | regulation of systemic arterial blood pressure mediated by a chemical signal | 45 | 2 | 0.0203784 | 1 |